I'm also just a hobbyist, but I say strip to bare metal, then coat the surface with a phosphoric acid based metal prep liquid. Leave it to react with the metal for 10 mins or so then clean it off with laquer thinner. The prep liquid serves to chemically neutralize any remaining rust you can't see and lightly etch the metal. Then comes your epoxy primer, then bondo, then spot epoxy prime over the bondo. Then if you want you can do a urethane surfacer primer, sand that smooth then hose on your actual paint. If you download and read the p-sheets for the line of paint/primer you want to use you can get an idea of what products can be used with what.