If the paint is coming off easily, you should take it down to bare aluminum. You can use a wire wheel on a grinder, sanding block, or aircraft stripper. Then, clean it and give it a good rinse and let dry.
Next, you need to prime the boat with a "self etching primer". I have used Rustoleum Self Etching Primer in rattle cans, which can be found at Walmart in the automotive section, or you could go to Napa Auto Parts or any other auto store and buy a self etching primer. Here's what the self etching rattle cans look like from Rustoleum:
After the boat is primed, it's ready for paint. You can use topside paints which are designed for marine use, or even go with a cheaper spray can job. It's really personal preference, just remember that non-marine paint won't last as long or be as durable. Personally, I think a jon boat is usually scratched and dinged anyways, so a flat green spray paint like "Rustoleum Camoflouge" is actually what I'm starting this week. Also, to get professional advice, don't hesitate to go to a local marine paint store and talk to the employees.
As far as filling holes, there are numerous ways to do it. Once again, it's about preference and how much you want to spend. You could take the boat to a professional welder, who might charge you $30 or $40 bucks for a very small job, to a few hundred if you have a lot of work to do. Other people use sealant, and various epoxy products or marine putty that can be filled, sanded, and painted which hides nicely under that new paint job.
Just an example of marine putty that you might consider:
https://www.iboats.com/Aluminox-Epoxy-Aluminum-Putty/dm/cart_id.911809534--session_id.691077081--view_id.38142
