Applying filler over urethane primer is not the way to go. It should be stripped to bare metal, prepped with 80 grit and sprayed with epoxy primer, then any filler work can be done on that. The urethane will not have the adheasion needed for supporting the filler.
The epoxy will provide moisture protection and the holding power for the filler.
It may be more work than you want, but it needs to be done. If it's worth doing, it's worth doing right, so it will last.