O'Flanagan/Maguire left Boho in about 1842

Mary Ellen,

Tradition was generally to marry in the bride’s church, and thereafter she’d attend her husband’s. In this case with a mixed marriage, that would have required the bride to change to RC. Not every bride did. Some families bought the males up the husband’s denomination and the girls the wife’s. Others adopted one or the other denomination. It varied from family to family. The RC church is unlikely to have married them unless Mary converted prior to the ceremony. But as I say, since tradition was to marry in the bride’s church, you might expect that to be Boho Church of Ireland.

Unfortunately the early Boho Church of Ireland records were all destroyed in the 1922 fire in Dublin. There are now no baptism records earlier than 1840 and no marriages earlier than 1847. For the RC church the picture isn’t any better. The RC parish boundaries are slightly different and Boho is in 2 parishes- Devenish & Inishmacsaint.  Neither of those two parishes has any records for the years you need.

Regarding the surname O’Flanagan, be aware that the O’ prefix (and also the Mc) is detachable in Ireland and often dispensed with. Consequently the surname Flanagan is much more common than O’Flanagan in Co Fermanagh. Looking at the 1901 census of the county, for example, there are 307 Flanagans but only 7 O’Flanagan (just 2 families in fact). So your ancestor was more likely known as Flanagan in Ireland than O’Flanagan.

Maguire is the most common surname in Fermanagh though only a small percentage were Church of Ireland so that may help a little. Looking at Griffiths Valuation for Boho (1862) there were 8 Flanagan households in the parish. (Nil O’Flanagan). 64 Maguire households. If you have the time, you could cross reference the 64 households with the 1901 census to see which were Church of Ireland.

http://www.askaboutireland.ie/griffith-valuation/index.xml

Few records exist for the early 1800s and research at this period will be tricky especially without any church records.