All I can contribute is the method I've used recently: Get a tube of hardware-store epoxy-and-hardener (Devcon comes to mind), mix it with some West System Colloidial Silica Adhesive filler 406 so that you end up with a thick a mixture as you'd like. I would stay away from the kinds that use a tube of hardener in favor of real epoxy, not polyester resin. Gouge out the holes until fresh resin is exposed and fill.
Sand/file down the filler until smooth. A small block of wood with some felt glued onto it can serve as a sanding block (using a block is essential). Work your way through the grits (wet-sand) until you hit 1500 or 2000. Get some Interlux Brightside Polyester 4359 marine paint
and its primer. Primer and paint
a couple of coats, sanding between.
After the paint
is thoroughly dry and hard sand again, using the block. Using a polisher (such as a Porter-Cable 7424 I believe) work it with some rubbing compound, finishing with a polish. Wax and call it a day.
The Brightside may not match the color exactly, but I have found it to be acceptable. If I were to give advise to the manufacturers it would be to include some specific facts about the gel-coat color they use so that the customer could duplicate it if possible. Would save a lot of trouble.