It's been a while since I was in the body industry, but if we broke through on a sizeable area, we would etch, some shops even use a 1k spray bomb etch on small areas, and like dodge71demon said, prime the area and over lap. "Bull's eye's" can occur if you don't have proper coverage and non compatible primers. If your breaking through, obviously you're high in that area, so putting some high build well into the lower areas is important or you're just going to sand your new primer off again.
A product we used from time to time was "spritz" or "feather-fill" it was like a spray on body filler that was put on after the body work was done (either etched metal or bare, cant recall). We'd long board that and then prime and block. Helped make laser straight panels.