Reading up on the epoxy fill method, my question: how deep do I drill my holes as to not penetrate the second layer of glass?
About 1/8". You don't have to drill all the way through the foam - just enough to get close. You can poke through the foam with the drill bit spun in your bare hands to get down to the second layer of glass.
Beware the point on the end of a standard twist drill. Don't trust yourself to hold the drill to the proper depth. Use a drill stop or a small piece of tubing around the drill bit to control the bit. It will have a tendency to lunge when it breaks through the first layer of glass.
If there is any sign of moisture in the material you're removing, after drilling all the holes, let the boat sit in the sun for several hours to dry out, or else all your work will be in vain.
What size drill bit is optimal for the job?
As small as possible, but still large enough for the nozzle of whatever you're using to inject the epoxy. Use blue painter's tape over everything!
(drill through it). It will save you a lot of clean up later.
Bottom line: be patient, be careful, do it right and you'll forgo a lot of aggravation and re-work. The end result will be worth it.