Yes you can use bondo over the epoxy, but I recommend using a Polyester Glazing putty , the brand of epoxy you used should have a compatiable polyester glazing putty .

Just sand the areas where it is need with 150 grit sand paper and apply the glazing compound.

And It will need to be re-primed to fill small pin-holes and keep your color from soaking up when sprayed.

Spraytech