I've sprayed gel a couple of times so I'll pass on some relevant advise. You mentioned separating the wax from the gel - just buy wax that doesn't have gel mixed in it in the first place, like this stuff: http://www.fiberglasssupply.com/Product ... coats.html
, scroll down to part number F57-2940. Mix up your first coat with the catalyst per the instructions. It will set up, however, the micro thin layer in contact with the air will remain tacky - that's a good thing because subsequent coats will adhere to it. I typically wait 30-45 minutes between coats. If you try to put on coats that are too thick, the gel will run. Don't be greedy, multiple thin coats work best. When you put your final coat on, go with a mixture of 50% Duratec High Gloss Additive, also available at Fiberglass Supply, part number F60-0175. The Duratec will make the finish coat very glossy, and it'll harden without a bunch of orange peel effect. It also causes the top coat to dry hard. Be careful not to spray with too much pressure or hold the spray nozzle too close to your work or it will cause dimples. I learned this the hard way. The good thing is that even if your finish doesn't come off nice and smooth, it can be sanded smooth, polished, and look great. Gel coat is forgiving, just have a good power sander. If you sand too hard, you may have to spray some touch up gel in places, this is pretty common.
Decks are tough to deal with. Gel coat will gum up the non-skid pattern in the decks. If you aren't concerned with class racing rules, you might consider sanding the decks smooth. Once there, you can either leave them smooth or try to replicate the pattern with a mold, as per previous posts. Here's another idea - you may consider leaving the decks white and just gel-coating the hulls below the decks. Two-tone hulls were standard from the factory in the 70's, and white on blue (actually a shade close to Tarheel blue) was one of the legacy combinations. If you leave the deck white, coat it with Poliglow and it'll yield a high gloss shine while preserving the pattern on the deck. I used this on my decks and the results were fantastic. Here's the Poliglow link: http://www.poliglow-int.com/
You can find some pre-mixed colored gel coats here: http://www.fibreglast.com/category/Resins
. They claim to be able to match 900 colors.
Let us know how your project turns out.