I'm not sure what size drill bit I use, but it's not too small and not too large. Usually pick one from the middle. I've done this numerous times now and so far each patch has held. Still using both boats and one has almost more gorilla tape than plastic!
I would suggest not bothering with patching the outside of the boat. It's just going to scrape off.
I'll typically remove whatever I need to from inside the boat. Drill the ends of the crack (make sure to go all the way to the end). Put a layer of gorilla tape over the crack. Heat it up with a pen torch, then continue the process by overlapping the layers of tape in opposing directions.
Good luck and remember to check with Jackson first. They have a great warranty policy and customer service.