No, don't waxoyl over the paint, otherwise whats the point of painting it?

You may as well have cleaned it up and waxoyled it and left it......
But then imo waxoyl hides problems and can be worse in a way. It all boils down to what you use the car for and how often, take mine. I cleaned my underside, primed, stonechiped and painted and that's it.
I use the car as my second car, only in the summer months and dont drive it in the wet (if I can help it) so I don't for see a problem.... and its been fine for a fair few months now