Evan,
Your query is a challenging one. There are very few records in Ireland for people who lived here in the 1700s and the likelihood of finding anything on your family is pretty low.
You say that your family were probably Scotch-Irish who moved to Pennsylvania in 1720. If so, their ancestors will have arrived in Ireland from Scotland in the 1600s. There was a big migration in the period 1610 – 1625, mainly as a part of the Plantation of Ireland, but there were other waves throughout the 1600s culminating in a big surge in the 1690s due to famine in Scotland. Something like 200,000 Scots settled in Ireland in the 1600s, representing 20% of the entire Scottish population. But you’ll realise that if your ancestors arrived in the 1690s and left in 1720, they were only in Ireland for 30 years, one generation at the most, and the likelihood of there being any record of their presence here at all is extreme low. John Simpson born in 1680 could have been born in Scotland. The family might have arrived in 1610 but even then they were only in Ireland for 110 years and it would be very unlikely that any records would exist, unless they were major landowners or otherwise of significance.I checked the Muster Rolls (C 1630) and no Simpsons are listed anywhere near Fermanagh then then which points to an arrival post 1630. There was actually only 1 adult male Simpson in Ulster then and he lived in Co Down.
You say that the family were Covenanters. In both Ireland and Scotland today, they are generally called Reformed Presbyterians. So that’s one of several Presbyterian denominations. Presbyterianism was established in Scotland in the mid 1500s, by John Knox. Scots settlers later brought Presbyterianism to Ireland and so if your family were of any Presbyterian denomination, lived in Ireland and in particular Ulster, then that does point to Scotch-Irish ancestry.
That said, as far as County Fermanagh is concerned, though lots of Scots did settle there in the 1600s, the vast majority were not Presbyterian. The settlers in Fermanagh mostly came from the Scottish Borders - where Presbyterianism had not become established by the time they left - a lawless area where few churches were able to function, and so they had no religious denomination at all when they arrived. They were called Border Reivers. Reiver is a Scottish word for a robber. (Google Border Reiver if you want more information). Many later became Church of Ireland (ie Anglican). So very few Presbyterians were found in Fermanagh. There were some, but not many. So that does not say your family didn’t come from Enniskillen, it just means it’s statistically less likely. There is one Presbyterian church in Enniskillen. According to my guide to Irish Presbyterian congregations there was a Minister there from 1677 onwards who was responsible for the areas of Monea, Enniskillen & Derryvullen. Sadly the congregation has no records earlier than 1817.
I do not know of any Covenanter (ie Reformed Presbyterian) congregations in Co Fermanagh in the 1600s or 1700s. There is 1 church there today in Enniskillen but I am not sure how old it is, and PRONI certainly don’t have any records for it. You could contact the church if you want:
https://www.rpc.org/enniskillen/
In the 1901 census of Fermanagh there were 65015 people in the county. 35,577 were RC, 30549 were Church of Ireland or connected denominations and just 1201 were Presbyterian. So not a very common denomination in that county (though it is very common in other counties of Ulster).
Researching in Ireland in the 1700s is very hard going due to the general lack of records. If you don’t know where they lived it’s a needle in a haystack. Ideally you need to know the person’s exact denomination and the townland or parish they lived in to have any chance of finding them, and even then there may not be any records for that location.
Possibly DNA testing may be a way of matching with others who have additional information about where the family originate. Family Tree DNA reportedly has more people with Ulster roots than any other company. That obviously increases the chances of finding a match. You might want to try them or, if you have already tested, you can transfer your results to them for no fee.
The North of Ireland Family History Society is running an Ulster DNA project in conjunction with FTDNA and can offer testing kits at a reduced price. http://www.nifhs.org (Go to DNA project on the website).