How I filled my holes
Bondo can work above the water line and uis cheap. Paint the inside of your holes (the wood core) with thinned epoxy. Don't get 5 minute epoxy, it's not water proof. Thin it with either acetone (drys faster but thins the resine to get better penatration) or denatured alcohol (drys a little slower, more working time). then you can bondo the holes, but what I did next was to put 3 layers of fiberglass cloth on the inside of the boat (using the epoxy from painting the wood core) to close off the inside of the hole, so even if the bondo would leak it won't get water into the core or the inside of the boat. Then when that hardened, I bondo'd the holes from the out side. I then put a coat of epoxy over the bondo (after sanding it) and the painted. Still can't see any signs of any problems with the repair done 3 years ago. Marine fiberglass repair putties may work better, and do cost more. I know Mitch Craft, South Seas, and Well Craft used bondo to fix areas where the fiberglass wasn't bonded to the gell coat, and then just sprayed gel coat over the repair and wet sanded. I know because that was my job for a while at South Seas. Good enough for the boat builders, good enough for me.