patts right marine tex is best, it chemicaly bonds to the hull and it comes in white grey and black, with a little care you can blend it in if your hull is one of those colors
I do it this way, tape the area off into a small square around the holes with painters tape and then apply marine tex to the hole, then cover the marine tex with wax paper and smooth it down. When it dries just pull all the tape off and then sand it down even with surrounding area. I've done it more than once this way and you couldn't even tell there was ever a hole there.