Catholic Church in Enniskillen before 1848

Statutory birth, death and marriage registration (in some jurisdictions called Vital Records) only started in Ireland in 1864, save for non RC marriages which were recorded from 1845 onwards. So you probably won’t find statutory birth, death or marriage certificates in Ireland for this family. For earlier years you usually need to rely on church records, where they exist. You obviously need to know the precise denomination in order to search the correct records. Not all churches have records for that period and not all are on-line. 

RC records are mostly on-line on the nli site:   

https://www.nli.ie/en/family-history-introduction.aspx

The baptism records for Enniskillen RC parish start in 1838. Marriages start in 1817. I have searched the records for Owen’s marriage to Margaret Maguire but did not find it. I suspect therefore that they didn’t marry in Enniskillen parish.  

You say that Margaret Maguire/McGuire may have been from Kinnally. That’s the RC parish of Knockinny. Unfortunately its records don’t start till 1855. Tradition was to marry in the bride’s church (after which she'd normally attend her husband’s). So if that’s where they married then sadly no records exist for the period you need.

You mentioned that Owen may have been from Clonoe. I can’t find a townland or parish of that name in Fermanagh.

Though most Irish censuses prior to 1901 have been destroyed, some fragments of earlier ones do exist including some for the 1821 census of Kinawley (Kinnally) which is partially in Co Cavan and partially in Co Fermanagh. The Cavan part has survived but the Fermanagh part has not. There are several Margaret Maguires/McGuires in the Cavan part but none of the right age to be Owen’s spouse.

http://www.census.nationalarchives.ie

In short I think that there may be not be any records for the parts of Fermanagh that you need.

Thank you for your research and response.