If the boat already has paint on it, you need to find out what that is. Or more correctly whether or not you can paint over it. Try the M.E.K. test, take a rag soaked in Methyl Ethyl Ketone and rub a spot on the paint. Keep the rag wet with MEK.Rub for about 10 mins.
Turn the rag constantly and watch to see if any of the paint comes off on the rag. If the paint does not come off, you can sand and prime, then top coat with any good two part polyurethane or epoxy paint system.
If the paint does come off on the rag then as Jim says you will have to remove it.
With regard to working on the deck The deck is most likely to be polyester resin You can use either polyester or epoxy for modifications.I do not know which epoxys you used on your wooden hulls. The West system is good as are Ciba resins or Shell resin systems. Which mod are you doing? are you removing the round hole and putting in the square hole with the nylon spacers?
General rule of thumb with polyester fiberglass hulls, if the structure is in good condition with no crazing, then sanding the surface with 220 grit paper and applying an epoxy primer followed by sanding to 320 grit then a good two part linear polyurethane will give you a finish that will last 10 to 12 years, stick with one manufacturer do not mix brands.
If you have spots that have the gel coat worn through exposing the bare fiberglass, build them up with resin and glass cloth and sand them smooth before applying your primer. Try to avoid using polyester body putty (Cataloy, Bondo)these things usually crack and craze due to movement of the hull and show up later spoiling your work.