I would stick the filler in first then epoxy over that just make sure the bare metal is clean.
Also just so you know there is a window of letting bare metal set without resanding it and that's about 24 hours more or less depending on the humidity.
You can paint your base clear right over the epoxy if you want and if it looks good after the epoxy is on and your happy with it, I would read the directions but 24 to 48 hours and don't have to sand the epoxy just put your color right over it.
Hard trying to help without being there.