Mageesdaughter,
Methodism did not get started as a separate denomination in Ireland till the 1820s. Prior to that your family would almost certainly have been Church of Ireland (ie Episcopalian).
The Freeholders list is a list of people with sufficient land to qualify for a vote. (So just a small percentage of the population, and mostly farmers). So there may be plenty of other Magees in Armagh at the same time, not listed there.
I looked at the 1901 census for Co. Armagh (the oldest complete census). There were 495 people named Magee/McGee listed. So a fairly common name, even after a century of death and migration.
If you can’t narrow the search to a particular townland or parish, probably the only thing to do would be to get a researcher to work through all the 30 or so Church of Ireland parishes in Armagh to see if they can find the marriage and baptisms. Quite a lot of Church of Ireland records were destroyed in the 1922 fire in Dublin but there’s still about 60% left. You might get lucky. Copies of the surviving records are held in PRONI (the public record office) in Belfast.