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I would fill a few holes in a few different spots, taking them to a completed stage. See how they look, and how long it took to do them. If you have even, say 250 holes, I think it will make more sense to fill the holes flush, and re- gelcoat the entire area. Matching the color on each of the holes is next to impossible, as you will find it changes from section to section. As far as a filler goes, I use System Three SB -112 Epoxy. It is the only epoxy that gelcoat will always cure to. It will not crack, and has the flexibility to expand and contract. You may, however, over time, see "ghosts" of your fillings. Good luck, better you than me, I have my hands full with 20 holes!