You can make permanent and completely waterproof repairs with an epoxy resin thickened with a filler. I have used WEST System epoxy to make minor repairs to small damaged areas on the hull that are underwater where the gel coat is abraded--which is what you have described has occurred on your boat.
I recommend buying a WEST System Repair Kit. These are very inexpensive (less than $25) and include all the materials--gloves, mixing bowls, brushes, fillers--you will need to make many small repairs. The epoxy resin and the hardener are provided in sealed foil packets, like ketchup packages, and provide the proper ratio for mixing. They have a very long shelf life. I recommend these in preference to any sort of pre-mixed, in a bottle, "epoxy" to which a "hardener" is added by the drop. Once the bottle is open the shelf life is very limited. Real epoxy resins tend to have mixing ratios of resin to hardener from 1:1 to maybe 5:1, not 100:1.
Repairs on the underside of the hull won't be seen. You can just repair them with epoxy that you have mixed with a white filler. You can get a reasonably good color match, but that is not really a concern on the bottom of the hull. One complaint you will hear about epoxy is the resin will age with exposure to UV (sunlight) and yellow. Yes, that happens, but on a hull bottom it is not a problem. How much sunlight does the bottom of a hull see? Also, if the repair starts as white and slightly yellows, it makes a nice match to the Boston Whaler Desert Tan gel coat--okay, not perfect but not horrible.
If the damage is extensive, you might want to consider flipping the hull over to work on the hull bottom. If there are only one or two areas to be repaired, you may be able to work on them from below, although working against gravity can be a problem.
More details are in my lengthy and detailed narrative at
The Epoxy Curehttp://continuouswave.com/maintenance-logs/epoxy/Epoxy is really perfect for this sort of repair. If the repair is in a highly visible area, the final coat should be a color-matched polyester gel coat resin with wax additives so it can cure in open air. You can buy small batches of this material from Spectrum Color. They make a gel coat patch repair paste, and offer it pre-tinted to match gel coat colors from Boston Whaler. Their use is demonstrated in a presentation at
https://www.youtube.com/watch?v=_SQY2_y4Zhw&t=4s