I use the method Ken described and it works extremely well. You want to make your holes slightly smaller than your outlines, then SLOWLY and CAREFULLY enlarge them until they fit the way you want. Plan on having the cowl on and off about 12 times before you get them right where you want.

I also suggest getting a couple of different grit TAPERED stones for your dremel and use the stones for the "fine tuning" of the holes. A big plus to the stones is that the finer grits will not chip the gel coat on fiberglass cowls. I normally use a dremel cutter for hogging the hole out to about 1/16" - 1/8" from drawn on opening. Then I switch over to the stones.

If the cowl is pre painted, consider putting masking tape over the areas you want to cut and draw your openings directly on the tape. Any residue left by the tape is easily removed with some alcohol.