I have already removed inner wheelhouse and media blasted the surface rust on the inner lip and the wheelhouse then covered both in epoxy on my 97 F350. I plan on using undercoating but my question is should I apply paint between the two then undercoat or just undercoat over the epoxy? Because this is a typical rust point on these trucks my goal is to seal everything and avoid having to do this again for a long time, as far as where the lips meet I'm thinking Lords fusor as a sealer so I can still weld them back together.

you do not need to topcoat epoxy with anything if you dont want to it will seal it enough on its own.

Wouldn't an extra coating help to protect the already weak point, or would it cause more problems. As I said before I want to avoid having to do this again for a long time. Thanks again

If you want extra protection, just spray another coat of epoxy. It's more
durable than any topcoat would be. You could also go heavy on the
undercoating in the problem areas.

What type undercoating are you planning on using? Rubberized bedliner
seems to work good in the fenderwells. It's also good at absorbing road noise.