So.....mission complete! Put in all the snaps and it looks great. A few helpful hints from my own lessons learned:
1. Keep two rags handy. One is dry and serves to clean excess caulk from the fingers. The second it damp to clean excess caulk from the fiberglass.
2. As suggested above, I drilled a pilot which was roughly 1/2 the width of the screw. I then used a larger bit (about the width of the screw) to drill a wider hull just through the gel coat. On the first couple of holes, I did not drill deep enough. The result was minor cracking of the surface. By drilling a bit deeper (one can see how deep the gel coat is by looking in the pilot hole) I was able to eliminate the cracking completely.
3. Before I seated the screws, I opened a small tube of 3M sealant and used one of the screws to crack the tube seal. I then simply dipped each screw down into the tube making sure to coat all the way to the screw head. In this way, when bedded, a bit of excess was pushed out of the sides. I used the damp cloth to remove excess.
4. Finally, be sure you know what's behind what you are drilling. I had a brief moment of terror when one of the pilot holes appeared to be pulling some kind of gray plastic. Luckily it was nothing. If nothing else, wrap a piece of electrical tape around your bit to indicate the depth of the screws. This will prevent drilling any deeper than is absolutely necessary.
5. Drilling holes for the stern seats was easier because of the plastic material but again, do not drill too deeply. One the bit got a bite into the material, it seemed to grow a mind of it's own. Again, tape as a depth guide will help here.