First, I'm sure you know this, but you can't drill the bottom if its tempered. If it is tempered and you need to drill the bottom, you can take off the bottom pane and replace it with 3/8 inch glass for about $60.
You need to remember that bulkheads have a rim around them that hold the washer. Flange I guess its called. A 1" bulkehead is about 2-2.5 inches in diameter. Do not drill your holes to close to the plastic rim or edge or your bulhead won't fit.
Now you need to decide how you want the tank plumbed. If your going to be placing close to a wall or veiwed from both sides, you'll want to drill the bottom so your drain can go directly into the stand. Your return can go over the back or it that's unsightly to you, you can drill another hole for the return. For this you'll need a overflow box that goes from the bottom of your tank to the top. You can buy these commercially or make on from black plexi and a router.
If you want to come out the back , you can drill holes in the back and put your durso outside and have a shallow overflow box on the top. This is a great option because the shallow overflow box is easier to keep clean and easier to get clownfish out of that decided to jump in.
You can put your overflow in the center or in the corner. Commercial tanks that you buy predrilled, usually have two corner overflows. The old thinking was to run huge volumes of water through a wetdry filter and back into the tank. This is a waste today in my opinion. I think one overflow is plenty. The most water I have going through my sump, is enough to keep the temperature stable (heaters and chillers are located in the sump) and enough to feed my skimmer. My skimmer has a 900 gph pump on it. I'm guessing it puts through ~600 gph because its restricted by a nozzle. So to keep from reskimming water, I want at least 600 gph going through my sump. Flow in the main is handled by a closed loop or power heads.
You can get better input on specific plumbing if you let us know what your design plans are.
Mike