Kim's got it, in my experience - the glazing putty is actually very thick primer, not filler like bondo, and meant to be used almost like a 'spot primer' on very minor imperfections
but to the original question - if the 'zits' are real holes, resand and fill properly or if minor, sand and reprime - you can use filler over good primer, especially epoxy, but the consensus seems to be it's best on bare metal
Bill