You said bondo, which is pink talc based filler. Bondo does make a marine fairing compound I'm pretty sure, but that is not for holes. fairing compound does the same thing to a boat as bondo does to a vehicle..
Lot of cheap fishermen will patch the holes from the outside. You have to scuff the gelcoat back to glass, and fiberglass a patch of 1708 biaxial cloth in a couple layers in with poly resin. That is still the wrong way to do it.. Correctly you need to gut the boat, and the patch gets put in from both sides. 2 layers of 1708 each. But it's still obviously rotted.. If you bought a $700 boat and it's only worth $700 to you, then no it's not worth it