Go with the two-part Polyurethane. Most of these, such as Awlgrip, are prepped with a two-part epoxy primer. As for brushing or "rolling and tipping", it can only be done well with the proper "extra" additives for the paint. Awlgrip can provide these and has great literature on this. But, I`ve been there and done that...without sprayin, its very tough and expensive - especially if you don`t get it right. However, there is a great alternative to professional spray equipment for a small surface area like the Hobie. The Preval (disposable)paint gun at Home Depo sprays the stuff beautifully and its cheap. You`ll need about three compressed air refills for each coat depending on the paint/film thickness. They are about 5 bucks each and its worth it. The Preval sprays the two-part primer and the polyurethane VERY well. I can`t say enough about it, particularily with the high-end, insanely hard to brush paints.
Now, some info on the paint itself. Two-part poly is harder (yes harder) more scuff resistant, more UV and impact resistant than gelcoat - despite urban myths to the contrary. Applied professionally it achieves a better and longer lasting gloss than gelcoat and does not oxidize like gelcoat - hence no waxing. This is why some high-end yachtmakers are pulling boats from the mold and painting them right off the bat. You pay big bucks for this though.
When applied to fiberglass AFTER the molding process, gelcoat DOES NOT adhere as well as the two-part poly and is prone to chipping and cracking. Not to mention it tends to be very labour intensive when applied "out of the mold". Also, it will not outlast the paint when applied in this way. This is because the paint forms a significantly stronger mechanical bond than the gelcoat. Gelcoat applied DURING the molding process will, however, have a stronger chemical bond than the mechanical bond of any paint that is applied after the molding process. Manufacturers use it (gelcoat) in the mold because it is much cheaper and less labour intensive than the paint. But its advantages of cheapness, labour, and longetivity only exceed the paint if it is applied during the molding/layup process.
Don`t be afraid to feel good about a well excuted paint job with top quality paints. But rolling and tipping is likely to leave anyone but a real pro somewhat disappointed.
As for the question on how to prep the non-skid area on the top of the hulls. First, spend the money on a top quality dewaxer/degreaser from an auto body supplier. B.A.S.F makes a great one - R.M. 900 I believe. This should be the first step on the whole boat (more than one application too). Then scuff your non-skid with a stiff but fine wire brush as best you can. After that, the two-part epoxy primer will hold on just fine as long as its clean...very clean.
Best of luck.
Hope my overly lengthy shpeel helpa ya out.