I use a dremel tool with a cutting bit, believe it's the 199 Dremel High Speed Cutter [DRE199] | Tools - A Main Hobbies
or one that looks like this. For smaller holes I cut in at an angle till I can get the cutter
horizontal and rout out the core. By going in at an angle, don't cut up much of the FRP top layer of the deck.
I tried allen keys in a dremel but the dremel just didn't have the torgue to swing it unless I ground the Allen key down so it was almost too small. The 199 Dremel bit worked so much better especially at cleaning
out all the core material. If you used a drill, an allen key will work better but chatters pretty badly and can bust the Allen key.
Once I've gotten the core cleaned out, use a syringe to squirt in resin and then suck it out. Figure the straight resin will soak into everything and insure a good bond. After I've sucked out the resin, add filler to about peanut butter consistency, refill the syringe with it and inject that in the deck. Leave it a little proud and sand down after it kicks.
I also chamfer the whole with a counter sink bit in my screw gun. That makes for a much better bond at the surface for the expoxy. Putting filler in a straight drilled hole sometimes cracks between the filler and deck which I assume lets water
into the core.