"... told the family his hometown was Kesh, Fermanagh."He may have lived near Kesh- people in the country often gave the name of the nearest town or village as their place of origin. The marriage certificate will give the exact location (townland).
"I wonder why Thomas & Mary chose to marry in the Civil RegistryOffice rather than the parish church. Could this suggest they did not normally reside in the Derryvullan Parish?"There are many reasons for marrying in a Registry Office- mixed marriage, bride pregnant, wanting a quiet wedding (recent family death, parental disapproval), own minister not licensed to perform marriages), etc.
The record you have purchased is a bit confusing but the town of Kesh is in Lowtherstown Poor Law Union (Lowtherstown is the old name for Irvinestown). Derryvullen civil parish covers parts of Lowtherstown and Enniskillen poor law unions.
http://www.thecore.com/seanruad to find details of places in Ireland
"Does anyone know of any online sites for Fermanagh graveyards, please?"There are links to lots of churches and graveyards under FERMANAGH RESOURCES at the top of this board-
http://www.rootschat.com/forum/index.php/topic,366887.0.htmlHowever, most will probably not be online.
To search for church records you'll need to know what religion the family was and for gravestones (remember not everyone put them up or they might not survive) it will depend on the denominations. If Protestant be sure to check Church of Ireland buryhing ground even if they were Methodist, Presbyterian, etc.