For small holes I used Marine Goop. Anything larger I would seek advice from the manufacturer. In many cases they will send you filler material to match. I once owned a Cobra kayak and had a crack on the end. I contacted Cobra and they sent me the plastic welding rods and instructions on how to fill it properly.
Also, if I'm not mistaken, many of the local kayak dealers will help you make the repairs for a minimal fee.