Preston is not a common surname in Fermanagh. In the 1901 census there were only 11 and some of them came from other counties. The main family I could find was this one:
http://www.census.nationalarchives.ie/pages/1901/Fermanagh/Enniskillen_Urban/Wellington_Place/1364839/
You have the benefit of knowing the head was born in Enniskillen c 1846. He married Margaret McCarter in Enniskillen in 1869. If you got their marriage certificate it should tell you his father’s name.
The family were essentially Church of Ireland . Unfortunately Enniskillen Churhc of Ireland lost its early records in the 1922 fire in Dublin and with a few exceptions, has no baptism records prior to 1861. This is what does still exist:
“Extracts of baptisms, 1667-1789, marriages, 1668- 1794, and burials, 1667-1781; burials, 1879-1907 and 1941-50;vestry minutes, 1731-1920; copy deeds, 1796-9; select vestry minutes, 1871-80; register of church members, 1871 and 1946-50; preachers’ book, 1895-1928.
Extracts from baptism, marriage and burial registers, 1666-1826.
Printed copy of Old Enniskillen Vestry Book, with extracts of births, marriages and deaths, 1666-c.1797.
Extracts from vestry minutes, 1666-1912, which include some baptism, marriage and burial entries”.
There’s a copy of the above records in PRONI (the public record office) in Belfast.
There are some Preston entries on the Fermanagh Gold site. You might want to work through them. See: http://search.atavus.org