Whoa....we need to know what brand, and what specific paint and catalyst.
Two Part Linear Polyurethanes are entirely different than epoxy paints. There are a number of additives which can be added to the base paint, as well as a catalyst. I suspect that you have "perfection".
For starters the boat should be de waxed--using a specific dewaxing solvent. Then the boat well sanded, and any defects repaired with epoxy filler. Next the boat need to be sanded again, then primed with two part epoxy primer, and finally sanded a final time, lightly before applying the two part LP paint. A special tac cloth is used just before you apply the paint.
I don't know what you mean by "sections at a time"--and you used about a pint of paint. Hopefully he did paint an entire side of the boat. There are a lot of tricks using two part LP, but it should be put on continuously overlapping, keeping a "wet edge". You don't want to paint half of a side of the boat. Preferably, you will paint the entire boat at once. The best method is "tip and roll, which often utilizes two people--one rolling the other tipping with a quality brush.
I have sprayed LP (A mast, with days of prep first). I have brushed LP, and Tip and Rolled LP=-mostly on decks and cabin house sides etc. For a hull I employ a professional. She has an assistant, who constantly tends the spray paint hoses, plus looks for sags, runs, holidays etc. She puts two or three coats on in a continuous setting. She also spends weeks getting the boat ready. When done, there is a paint job which looks better than the gel coat--and will last at least 10 years, without waxing. This is expensive.
The best for an amateur to start with is something like TopLac or Brightside (one part)--the two part is called "perfection". Note that most if not all of the two parts recommend application over an epoxy primer. A quart of perfection is about $85 and of Brightside about $45. You really don't want to paint a fiberglass boat until the hull gel coat is pretty well gone.....
Sunbeam is correct--this is toxic stuff. The gal who does our work, wears a suit, plus an external air supply. The charcoal canister type of respirators (which I also use, for small jobs) is OK--but better to have a professional clean air source. You want goggles, a knit stocking cap, and then a full tyvek suit (I wear these for bottom paint and epoxy also). The head sock costs about $2 and the suit about $10. (less in quantity) The respirators start at about $40 and go on up.