Michael,
It depends on how much you've burnt through the gel coat. I'm starting to paint my tail surfaces and you can see the process I'm using.
I also previously finished and painted an entire fiberglass kit car (Factory Five Racing, Mk3.1 Cobra replica) and you can look through my photobucket account for my finishing if that helps.
http://photobucket.com/albums/nn218/STL-Scott/FFR%206583-Build-FrameI would use a polyester surfacing primer first, something like slick sand, which is a high solids, high build sandable primer surfacer. You can sand this just like the gel coat. You then want to hit any low spots with two part light weight body filler, then seal it all down with a good 2K epoxy primer. Next is a light wet sanding of the epoxy if if you have any orange peal in this coat, prior to paint. You can either use single stage 2k paint, or base coat, clear coat. If you want to go cheap rattle cans work but I'm not a fan of their durability.
Let me know if you have more questions.