Really need to know more about your problem, you shouldn't need to waterproof fiberglass, just where it is penetrated. The top coat is for UV protection not waterproofing. Last year I rebuilt a fiberglass cedar strip canoe, I built twenty years ago. I didn't use marine epoxy and it got weak and crumbly over time. I added an extra layer of fiberglass cloth and marine epoxy on the bottom, then re-enforced the inside with strips of epoxied carbon fiber and Kevlar. You can find everything you need to know about fiberglass repair online, check out boat building sites, your top is basically an inverted boat. Marine paint would give you an excellent protective top coat.