First I would drill out the holes slightly oversized to remove any sealant. Next, dish the surface around each hole (you can do this with a large countersink). Fill each hole with 3M Premium Filler or thickened epoxy. After the filler cures, sand the filler flush and then sand the entire area with 150 grit. Mask off an area larger than what you want to paint. Spray color matched gel coat on the surface. Don't spray all the way to the masking and you won't have to worry about the hard edge of the tape line. Be sure to catalyze the gel coat. Here's a trick that not too many people know. Instead of adding wax to the gel coat, I spray several very, very thin mist coats of PVA over the still wet gel coat, waiting a minute or so between coats. PVA is water soluble and comes off when you wet sand. I think it leaves a better surface than wax and doesn't require as much wet sanding to get a good finish. If you spray it too heavy, it will just run off. If your supplier has a broad enough selection, you may be able to buy patch booster (aka patch aid or patch thinner). If you can get this you don't need to worry about adding wax or spraying PVA over the gel coat. Patch booster has surfacing agents built into it. One caveat about patch booster - it needs to be fresh.