Need to have two holes in my roof repaired - Jayco 1206

I would definitely go with the Eternabond on the top but you need to fill in the hole with something to give the Eternabond support underneath it. Fill it with two-part epoxy or something so you end up with a surface relatively level with the roof.

Some people use white caulk (nothing found in a hardware or big box store, use dicor or similar from RV dealer) to go around the edges of the Eternabond to dress it up. Personally, I don't care as I know it's doing its job well.