about anything can be used, you don't really need to "fill" the holes. If you are trying to rebuild the boat back to a beautiful state, then you should plug each side with some fiberglass and resin, then sand it smooth and paint to match. If you're not concerned about it looking proper, go with some quality silicone, filling the holes completely, let it dry. Make sure the holes are dry first as the silicone will not stick to a moist surface.