RE: How to repair GEL coat?
If the damage is minor, you could do as you said and fill it. I would sand the damaged area to remove any loose bits and fill with a feathering polyester glazing compound. You can then wet sand the area, prime and paint. If the damaged area cracked the fiberglass, you may need to sand the inside of the affected area, clean with denatured alcohol and reinforce the area with some 3 to 6 oz cloth and a good laminating epoxy system prior to the cosmetic repairs.
A few pictures of the affected area inside and out would help in deciding what may or may not be needed.