My 17-year-old just used his own money and bought a new 12 ft Prowler Jon boat from Bass Pro. We'd like to add a couple of handles to the back to make it easier to carry and probably tow a kayak. Has anyone done this? I'd like to get some ideas from people who have already done it before I start drilling holes in this boat.

Not the same model, but we added handles to my neighbor’s little Sea King 12 footer. He found some really nice stainless grab handles from McMaster Carr, and we drilled and mounted with 1/4-20 stainless steel hardware.
 

Use a good sharp twist drill (do NOT under any circumstances use the ones with the built in pilot - they will mangle the plastic) and add a dab of silicone to the holes before pushing the bolts through and you shouldn’t have any problems. Use stainless fender washers on the “interior” side of the transom and a dab of antisieze and you should be golden.