You're going to want to locate the spot you want it and double check the back to make sure that it's in the clear. As simple of a step as it is, it's easy to overlook and drill through and into wires, or a fuel line or even worse, somehow locate it in a spot that you can't get the hose on the back side. Once you've done all that, you're going to want to lay out the hole on the outside of the hull. You're going to want to use either masking tape or some painter tape to cover the entire area and then some that will be drilled. Once that's down, you can draw out your hole and cross hairs so you can make sure it's where you want it. The tape will also help to prevent the gel coat around the hole from chipping.
Once layout is all finished, then comes the part that just about every glass boat owners cringe about....drilling a hole in that beauty. Given that this is something that you really don't want to screw up start off drilling a small pilot hole in the middle of the cross hairs that you laid out. The small pilot hole will help you to prevent your hole saw from walking and also if the small bit walks or you don't get it right where you want it, you can adjust it easily. (your pilot hole size will depend on what bit you choose to use for the big hole)
Now for drilling the bigger hole. There are a few different bits you can use to drill through fiberglass. A hole saw is probably the best option if you can find one that small (bi-metal is better than wood). A sharp spade bit will do the job as well as a sharp fostner bit will also. Line up the guide bit of the hole saw with the pilot hole and start your drill in REVERSE. Watch the dust/shavings coming from the bit as you run it backwards as gel coat will be a white color. Keep drilling in reverse until the bit has went completely through the gel coat and into the fiberglass itself. Usually the fiberglass dust will change colors when you hit it and when you do, stop and put the drill in the forward drilling position. Make sure you don't force the bit through, just go slow to prevent heat build up and let it do it's work. Also, you don't want to force it because it will have a tendency to blow the back side of the hole out leaving it uneven and no longer a uniform thickness.
Once the hole is drilled, check for fitment. If it's good, remove the tape, but don't pull it straight up. Pull it from the edge towards the hole folding it over itself. This way it's not lifting up on the gel coat surface, it's just pulling it. towards the hole. When you're done, you should have a perfect hole without any chips in the gel coat. Running the drill in reverses is what really helps prevent that so be sure you do that. Before installing the bulkhead be sure to seal the open fiberglass pores with silicon and also when you put the bulkhead in put silicone on the surface that will be mating with the fiberglass to keep moisture out.
I know that probably seems like a book for something as simple as drilling a hole. It's really not that complicated, but I've seen some bad holes where the gel coat is chipped all the way around and it looks like crap. Your bulkhead should cover most of these if they happened but it could lead to some funky looking spider cracking if it chips out too far.
