I had the same questions when I purchased my duckboat, which is a fiberglass hull. I got a lot of great advice from this forum, this is what I did.
I purchased a gallon of FME (Flat Marine Enamel) from Lou Tisch (Lock Stock & Barrel, he is on this forum), it was #28 Dead Grass Green. The paint costs more than most, but you certainly get what you pay for, outstanding product! Lou also provided me with step by step instructions for surface prep and application.
Basically, I sanded the entire hull down, used a solvent to remove anything else then painted the entire hull with 2 coats of FME. I brushed it on, but instructions are also included for shooting the FME. The first coat goes on thin, the 2nd coat goes on thicker. The FME wears like iron! I have had this boat through ice, up against docks, rocks, etc and the FME doesnt chip or scratch!
To finish off my boat, I bought black, brown & tan Parkers spray paints from Cabelas, along with a stencil to spray on a pattern similar to Mossy Oak Wetlands. The black "bark like" pattern went down first, then some brown reeds, followed by tan reeds over the entire boat. Of course I grass the entire boat for duck season, but the camo pattern below certainly helps.
Here are some photos of the entire process:
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Boat as originally purchased
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Sanding the hull
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Painting the hull with FME #28 Dead Grass Green
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Finished product
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Another shot of the boat finished