Here is the way i do bondo/body work. And i consider this to be the absolute best way to do it for the longest lifetime of the paint job. First is strip any old paint off by hand, then sand blast. stripping by hand decreases the chances of warping the panel when blasting. Before blasting, i do any metal work that needs to be done, patch panels, metal work, and all welding. then blast it. Once the panel is blasted, i immediately (within an hour) coat it with Etch primer. Etch primer has acid in it that neutralizes micro rust (rust you can't see). It will NOT neutralize dark rust spots or surface rust, it needs to be good clean metal. After 2 coats of Etch, wait 15 minutes, and then seal it. I use a very expensive primer called NP75 from sherwin williams. Any paint rep will tell you it is one of the most badass primers on the market. I had an Dupont rep tell me one time that he wishes they could make a primer as good as it. NP75 is an epoxy/Urethane hybrid that is a sealer and high build in one. It is DTM, which is the epoxy side of things, and has the build and lays out slick like a Urethane. but really any Epoxy sealer would work just fine at this stage also.
Once i seal it with the np75, 2-3 coats, I then go back and SCUFF my bondo areas with 80 grit, being careful to not break through to metal. Don't ever apply bondo without scuffing. Bondo gets its adhesion from the mechanical bond of the sanding scratch. I do my body work, and get things ready for the next round of primer. Before i spray my next round of NP75 for block sanding, I then spray over my bare metal spots again with etch primer. Once you sand through and get the old etch off, the corrosion prevention is gone, so you need to re apply it. Then wait 15 minutes again and apply the NP 75, and do this repeatedly through my multiple blockings, until i have the panel laser strait and ready for paint.
this is the only way i can see doing these paint jobs that will guarantee my customers the best bang for their buck. I don't want to see any of my jobs having rust bubbles 5 years later because i didn't use the best possible methods for rust prevention, and allowing my body work to have a long of a lifetime as possible. My gallon of Etch primer cost me $325, and is worth every penny of it for the insurance. I have done paint jobs without it before, properly stripped, and immediately sealed and within a couple of years it had some minor rust spots coming up, which i took care of for free because i value my customers. But this is just my .02 cents, and i realize i have a biast opinion on this because this is how i make my living. I'm not the average joe at home just trying to do a paint job on a budget.