mainsail's approach is the ideal
Sealing Deck Penetrations to Prevent Core Rot Photo Gallery by Compass Marine at pbase.com
1) use a dremil bit #115 to shape the hole(see above link)
2) tape underside
3) fill hole with unthickened epoxy, via syringe
4) let sit for 5 minutes
5) remove unthickened epoxy via syringe
6) fill hole with thickened epoxy
7) let cure
8) paint with colour match paint via q-tip
Yes counter sinking the hole is good, asuming you plan on drilling the hole out. Using a counter sink bit will help to prevent the gelcoat from chipping.
Yes thicken the epoxy, straight epoxy is brittle and should be "softened up" a bit. Particularly if you ever want to sink a screw into the filled hole in the future.
A suggestion, find a hole puch just larger than the hole to be filled. Punch a hole into tape and place around hole. After filing hole with thicken epoxy, remove tape. The tape will "catch" any overflow thickened epoxy, allowing for easy cleanup.
I am a novice at this so see the link to mainesail's site, follow his advice and you can't go wrong.