<---- worked in teh body shop for the last 5 years ... listen up
if you have panels that are starting to rustbuble and such, the VERY BEST way to repair the rust spots is to grind them, sand blast any little craters that are left from the rust ..... use a VERY high quality primer over them like PPG 271/275 .....
then just sand that w. 80 on a DA and bondo over it ..... i SWEAR that bondo will stick to todays high quality primers, just prime over everything again when your done to seal it up
The real reason for the idea that you have to apply bondo to bare metal, THEN prime over it is cause back in the day when body filler was still an undeveloped product that was a PITA to work with, it wouldnt stick to paint and it blead through to the paint, (yellow spotting) so shops would save all the primer for ONTOP to try to seal it real good, but that was only laquer primer ..... which is fawkin worthless too
grind, primer, bondo, sand, bondo, sand, primer, guidcoat, sand, if its as straight as you want ... its ready for paint
good luck man