scuff top layer with 400 wet dry or scotch brite to remove shine off clear coat and also any wax's
fix dents then prime , block , prime , block til its straight. then paint
if you have waves etc in the panels, use a higher grit like 280 to get more straight then prime over the top.
no need to go back to metal unless fixing a major dent.
etch primer isnt usually much of a sealer either, so if it gets wet it can still rust.