autobodystore.com has a "classroom" and discussion board that goes over this dilemna in detail. you've got to watch what you put to inhibit rust (they like "picklex") because some of the stuff is incompatible with etching primers. i'm doing the same, strip to bare metal, fill and some day epoxy prime. in the meantime i'm using eastwood's metal prep and have had really good luck in keeping the flash rust at bay.
The procedure, as I understand it, is first strip, do rust treatment and then the panel repairs, epoxy prime (PPG dp40lf, for example), two or three coats of surfacer (ppg k36 or k38 for example), apply guide coat and block sand the living daylights out of the thing and then you're ready for your base/clear. Note that the epoxy primer must be topcoated within a week or it loses it's "bite". It's not the end of the world, you just need to scuff it and give it another coat.
