If the damaged area has a gelcoat finish, then the correct way to repair it is with gelcoat, not paint. If you have structural damage, i.e. the fiberglass is cracked or delaminated, the damaged area must be removed, then new fiberglass laid up and sanded smooth. Gelcoat should be color matched to the surrounding area and sprayed on the new laminate repair. It will have to be wet sanded and polished to make it look like the rest of the boat. Do not use filler to make a structural repair, it will crack. You really need to find an experienced fiberglass repair shop to do this type of work correcly. What you described is not the correct way to fix this type of damage.