Both ways work. Someone a while back did a study of sorts. Put down the filler on a bare prepped metal sheet, and did another over properly cured and sanded epoxy primer. Put it through several "tests"...bending the sheets, hitting with hammers, etc and the results looked pretty much identical in both test pieces. I have done bike frames in epoxy just to keep the rust from continuing (customers jobs that had set around awhile or were handled extensively). Left them in epoxy till I had the tins ready, then did the filler over the epoxy. Couple of them have been done 5yrs+ with no issues. I think it all just comes down to PROPER prep before any step is done. Good luck! Donny