There are two main, long-published accounts of the Irish origin of Bowe/s, both of which trace the names to Munster. One attributes the names' Irish origins to the Corca Laidhe and the other to the Eoganachta. Both accounts are essentially heresay in the absence of primary records and/or genetic proof. So far our surname study, using historical documentation and DNA research, has been unable to prove either of the Munster accounts, but some historical patterns are emerging to help explain their origin if not their truth.
To make matters more complex, the Irish Bowe/s name is believed to be a variant of Bogue, for which there appear to be a number of separate families from different areas, since it derives from the personal name Buadach, meaning "victorious." If there is a phonetic link between Bogue and Bowe/Boe/Bowes/etc., it could have occurred in more than one place. Meanwhile, the Bogue of Cork are, according surname historians and scholars, from the Corca Laidhe tribe, but they consider themselves to be Sullivans from the Eoganachta! So our work is cut out for us.
1418-1849 - O Donovan and the Book of Lecan
The first notation concerning the origin of the Irish Bowe (and variants) name occurs in the Book of Lecan, a transcription of even earlier works that two Irish scribes completed by 1418. This work covers the history and topography of the Corca Laidhe, an early, non-Gaelic, Erainn "tribe" (more accurately described as a tuath or petty kingdom to convey its political, not familial, focus).
Although the evidence is sparse, before the eighth century A.D. what is now Co. Cork appears to have been populated mainly by tribes of Érainn descent, including the Corca Laoighde tribal grouping of whom the Uí hEidirsceoil [O' Driscoll] were the chief family. The encroachment southwards of the Gaelic Eoghanacht of Cashel from the eighth century on resulted in the assimilation or displacement of all of the original Érainn tribes. In the case of the Corca Laoighde, this displacement was towards the southwest of the county, into an area which later became part of the diocese of Ross, roughly defined by the modern towns of Roscarbery, Skibbereen, Schull and Baltimore. 
The renowned Irish scholar John O Donovan, Esq. translated the Book of Lecan from Middle Irish in 1849. The source doesn't refer to our modern study names, but rather to an old Gaelic personal name, Buadhaigh, meaning "victorious." In the section "The Hereditary Proprietors of Corca Laidhe" the Book of Lecan scribes identify one such individual among the Corca Laidhe who became the progenitor of a sept called the Ua Buadhaigh. In his footnote O Donovan references Thomas Swanton, Esq. of Crainnliath, Ballydehob, Skibbereen (in Corca Laidhe territory), adding:
Ui Buadhaigh, now Baig, the g pronounced. They consider themselves Sullivans—T. S. 
1960 - Edward MacLysaght
In 1960, the Irish surname historian Edward MacLysaght, referencing O Donovan and the Irish surname historian Patrick Woulfe's early works reiterates:
The [Bowe] sept was located in the Corca Laoidhe country and O'Donovan says that they considered themselves to be a branch of the O'Sullivan's who had adopted this alternative surname. Woulfe, however, states that there is no such kinship. 
1967 - Patrick Woulfe
Patrick Woulfe follows with an updated work in 1967 where he infers that Baig in the Book of Lecan is the Irish precursor to the later anglicization of Bogue. He also attributes a number of other surname variants—including modern ones we are studying—to this origin:
O Boey, O Bowe, O Boye, O Bwoy, O Boige, Bowie, Bowe, Buie, Bwee, Bowes, Boyes, Boyce, O Boyce, Bohig, Bogue, &c.; des. of Buadac (victorious); a very scattered surname, but most common in Donegal, Kilkenny and Cork. In the last-mentioned county, the final “g” is sounded; hence the early angl. form O Bowige and the modern Bogue. The family is a branch of the Corca Laoighdhe, but was erroneously supposed to be a branch of the O'Sullivans, on account of the prevalence of the Christian name buadhach in that family; and it is not improbable that some of them have adopted the name of O'Sullivan or Sullivan. 
We can't be sure that Woulfe has accurately attributed our modern variants under study to the Corca Laidhe. The introduction to Woulfe's work indicates he collected information from clerics, lay people and scholars through his work, travels and communications. Also "newspaper reports, personal observation, lists received from different parts of the country, the writings of Dr. O'Donovan and Father O'Growney, etc." No doubt much of his information is true, though it's only as good as his sources and there are bound to be errors. His books don't tie specific information to its source so there is no way to verify accuracy.
Thirteen years later, in 1980, Edward MacLysaght (who shows in his introduction a detailed grasp of available sources from antiquity to his modern day) has this to say about Woulfe's first work from 1923:
Sloinnte Gaedhael is Gall is a most valuable work, based as it is largely on that of John O' Donovan eighty years earlier, but Father Woulfe makes the mistake of attempting to give derivations for almost every Gaelic name in the book: many of these are guesses and, as that great authority, the late Professor M. A. O'Brien, often mentioned to me, quite untenable. Today we have the advantage of being able to consult both scholars and printed sources not available to Woulfe fifty years ago, notably the Royal Irish Academy's Dictionary of the Irish Language. In some cases where I had little doubt that Woulfe was right I found competent scholars in that field rejecting his interpretation. 
The Sullivan Matter [FIX CITES]
NB While we see in the 1659 "Census" that the both the hard and soft "g" pronunciations appear to have been used in Corca Laidhe territory (in spite of surname historians noting that the soft "g" evolved in the midlands), the Sullivan association hinges on Bowe deriving from Bogue outside of Sullivan areas.
The Sullivans were part of the Gaelic Eoganachta tribe that gained power in the 8th century and pushed southwestward from their base in Cashel, both assimilating and displacing various Corca Laidhe families. It's not hard to see how after many generations of the original Érainn and invading Gaelic tribes occupying overlapping territories, no doubt intermarrying, family origins with either the Corca Laidhe or Eoganachta might become confused and obscured. To aid in the mix-up the Eoganachta reconfigured their early genealogies to advance their political, territorial and economic aims. Possibly confounding matters, separate Bogue families could have arisen from within both the Eoganachta and the Corca Laidhe.
According to the "Eoghanacht Genealogies" the Gaelic O Buadhaigh sept descends from Oilill Olum, the king of Munster who controlled all of southern Ireland in the 2nd century. The sept appears as a minor branch of the O Sullivans in this passage:
Maolodhar son of Sealbach had five sons: Ealathach, from whom the Mac Ealathaigh [Healy] family; Buadhach, from whom the Ui Buadaigh (O' Bogue); Cathalan, from whom Ui Chathalain (Cahalane); Maoilin, from whom Ui Mhaoilin; and Croinin, from whom the Ui Chroinin family (O'Cronin) 
The "Eoghanacht Genealogies" were transcribed from the Book of Munster (also called the Psalter of Cashel) in 1703 by Rev. Eugene O'Keeffe, parish priest and poet of Doneraile, North Cork. This is potentially as problematic a source as Woulfe. The Psalter of Cashel was first compiled in the late 9th century during a time when monks were reconstructing ancient texts. The ancient texts are now largely gone and the literature we are left with is considered by modern scholars to be part fabricated but also part truth. 
The genealogical section of the Psalter of Cashel was probably drafted c.900 by Cormac mac Cuilennáin, the bishop-king of Cashel. For Munster it draws mainly on records compiled c.740. The Psalter was updated c.1000. After a limited update c.1015 the Psalter was further edited by northern scholars in the eleventh century. Copies reached Leinster in the twelfth, and were included in Rawlinson B.502 and the Book of Leinster. The main stages of compilation are reflected in changes in genealogical doctrines, as the secular genealogies and the genealogies of the saints of Munster show. This section of the Psalter probably contained narrative material as well. 
The portion of the "Eoghanacht Genealogies" that contains the passage above about O' Buadhaigh is said to be taken from a poem by Cathan O'Duinnin written in 1320.  But what was the poem based on and where can we find a copy? Is what we have in the "Eoghanacht Genealogies" an accurate transcription of the poem? Why did O'Keeffe rely on the poet for this section. Was the work the poet himself relied on absent? Maybe it had been oral tradition.
1. O' Keeffe, Eugene. “
The Book of Munster. 1703.
2. O' Croinin, Daibhi, Ed. A New History of Ireland, I, Prehistoric and Early Ireland. Oxford University Press: Oxford. 2005, pp. 186-7.
3. Jaski, Bart. "The genealogical section of the Psalter of Cashel," Peritia, Vol. 17-18, 2003-4, pp. 295-337.
4. O' Keeffe, Eugene. “Eoghanacht Genealogies,” The Book of Munster. 1703.
In a closer reading of the part fabricated/part truth "Eoghanacht Genealogies," an ancestral generation of the Sullivan O Buadhaigh is found in which: "These four were sons borne to Corc by Aoibhinne, daughter of Aonghus folg, king of Corca Louighodhe". According to this passage, the Corca Laiodhe tribe married into the Eoghanachta tribe before O'Buadhaigh's generation, but it is just the kind of passage the Eoganachta were noted for fabricating.
A look at the 1659 "Census" reveals that O Buoige (11) and O Buoy (38) are principal names in West Carbery, Corca Laidhe country. This offers some strong support for Woulfe's account stating that at least some Bowe and similar variants like Boey, derive from Corca Laidhe Ui Buadhaigh/Buaig/Bogue, while adding some fuel to flame the Sullivan quandary. But is also suggests, contrary to Woulfe's commentary, that if O Buoige and O Buoy really refer to the same family and both arise from Ui Buadhaigh/Buaig, that early pronunciations in Cork included both soft "g" and hard "g." If the soft "g" wasn't a regional difference emerging in the midlands, why did the soft "g" branch from Cork end up there? But we also find Sulevane (27) in East Carbery and Sullivane (37) in West Carbery. So are the 11 O Buoige and 38 O Buoy descendants of Corca Laidhe O Buadhaigh or Sullivan O Buadhaigh?
There is an 1893 reference to "Ballyvogue, Baile ui Buadaig, 'the O'Buadhaigh's town'" in Kilmoe Parish.  This is seen today as Ballyvoge ("v" often substituted for "g") on the western peninsula of Corca Laidhe country. In 1980 Edward MacLysaght, the First Chief Herald of Ireland, prepared a map showing "the location of ... Gaelic septs ... in the period after the Anglo-Norman invasion and before the upheavals of the seventeenth century." On it, Bogue are located in Carbery, Corca Laoidhe country, but—probably erroneaously—not where Ballyvoge is now found. (See bottommost arrow on the map.) [4 FIXXX] Is "Ballyvogue, Baile ui Buadaig, 'the O'Buadhaigh's town'" an early Corca Laidhe O Buadhaigh settlement or a later Sullivan O Buadhaigh settlement?
Maybe helping to clarify this is the identification in the Eo´ganacht Septs DNA project at Family Tree DNA of O Bogue with the Eoganacht Raithlind, who are located well east of Corca Laidhe country on this map. If there is a Sullivan Bogue family, it should be situated there, not where we find "Ballyvogue, Baile ui Buadaig, 'the O'Buadhaigh's town'" in the heart of Corca Laidhe country."
The surname scholars' account of Corca Laidhe Bogue origins notwithstanding, many Sullivans still consider themselves former Sullivan Bogues, and no doubt some Bogues still believe they are Sullivans. As recently as about 2008, a parish records researcher focused on records around Cork city had this to share by email:
Bearers of a very numerous surname began using a nickname as a substitute for their original surname. This frequently happened in County Cork in the case of the Sullivans, some of whom, including several families in the Carrigaline area [south of Cork city], began calling themselves by the nickname ‘Boohig’ or ‘Bogue.’ Bogue was very widely used, in speaking, in ‘my’ five parishes [Passage West, Carrigaline, Douglas, Tracton, and Belgooley]. That is, people who now call themselves Sullivan remember that their parents and grandparents were referred to by one and all as Bogues. Or, rather, that everyone in the area knew that the names were interchangeable. Certainly, however, the name Bogue was understood to be a nickname of sorts, not a full-fledged surname. While most Bogues have now returned to the name Sullivan, some have not ... and it is possible that bearers of the two names are no longer conscious of the relationship.
It was unlikely that a Cork-born priest would write down the name Bogue when an individual said his name was John Bogue. ‘Bogue’ was not a ‘serious’ name, and it rarely got into the parish register. The priest would automatically have written John Sullivan. (There are exceptions.) ... This was the case with many names ... One must not forget that anything sounding too Irish had come to be associated with low class ... When Irish was still spoken, it was considered rude to speak to one’s parish priest in Irish. [Emphasis added.]
From Munster Bogue to Midlands Bowe
The 1659 "Census" shows plausible phonetic cousins, closer to our modern variants, as principal names elsewhere in the south: Boe (7) in Tipperary, Boe and O Boe (22) in Kilkenny, Bowe and O Bowe (12) in Queens (Laois), and O Boe (10) in Wexford. 
By the mid-19th century the geographic focus of these variants outside of Cork would suggest these surname spellings originated in Tipperary/Laois/Kilkenny.
It's true the names could have arisen completely outside Cork or Munster and there are competing theories worth considering. But it's also possible the sept started in Cork and the Bowe and Boe spellings arose and stabilized later in Tipperary/Kilkenny/Laois. William Carrigan provides the missing history that can explain—but not prove—an early migration of Corca Laidhe Buadaigh/Buiag/Bogue to become the midlands Boe/Bowe/Bowes.
[ADD CARRIGAN HERE]
1. Driscoll, Dave. “Origins of Our [O' Driscoll] Surname” (http://www.odriscolls.me.uk/origins.htm Accessed: 4 September 2010).
2. O'Donovan, John, Ed. "The Book of Lecan." Miscellany of the Celtic Society, Dublin: Printed for the Celtic Society, 1849, p. 50, footnote w. (http://www.archive.org/download/miscellanyofcelt00celt/miscellanyofcelt00celt.pdf Accessed 4 Jan 2011).
3. Journal of the Cork Historical and Archeological Society, vol. 2, 1893. (http://books.google.com/ebooks/reader?id=rgcMAQAAMAAJ&printsec=frontcover&output=reader&pg=GBS.PA234 Accessed 4 Jan 2011).
4 FIXXX. MacLysaght, Edward. The Surnames of Ireland. Irish Academic Press Ltd.: Dublin. 1980, Map. "Prepared by [MacLysaght ] and drawn and lettered by Nora O'Shea, one time heraldic artist to the Office of Arms, Dublin Castle."
5. MacLysaght, Edward. More Irish Families. O' Gorman. 1960.
6. Woulfe, Patrick. Irish Names and Surnames, Collected and Edited with Explanatory and Historical Notes. Genealogical Pub. Co. 1967, p. 447.
7. MacLysaght, Edward. The Surnames of Ireland. Irish Academic Press Ltd.: Dublin. 1980.
8. Pender, MA, Seamus, Ed. A Census of Ireland Circa 1659 With Essential Materials from the Poll Money Ordinances 1660-1661. Dublin: Irish Manuscripts Commission, p. 227-8, 2002.
9. Thanks to Howard Mathieson, publisher of the GeoGenealogy website for this map.