if you are going to do it with the tank full here is my recommendation; ( i am assuming your tank is pushed up against the wall so you cant drill from the back)
1. drain the tank to as low as you can get it - you want to be comfortable working or you will mess it up. Move your stacked rock if needed.
2. get some of that rigid pink sytrofoam insulation that everyone uses under their tanks. 1/2\" stuff is like $10 a sheet at home depot. Measure the inside length and width of your tank and cut a piece so that it fist perfectly in your tankwhile floating over the lowered water line. It should be snug enough that you need to push it down - it shouldnt just fall into the tank. Dont worry about water contact - its inert. This will section off your tank from your work area and provide a good working surface. Tape the stryofoam to the glass all the way around so theres no gaps between the glass and stryofoam. Use painters tape so you arent left with tape glue everywhere.
3. Go to princess auto and get the glass hole drill bit you need. Buy a new one - dont borrow one. THe bits have a limited life span and the cheap ones are even more limited. You will reduce your chances of cracking/chipping the glass with a newer drill bit.
4. Make a template - everyone misses this step and gets a jagged $hitty cut. Take some 1/4\" or 1/2\" plywood - drill a hole into that is the exact size of your glass drill bit. You can find cheap hole saws at princess auto or borrow one - everyone has em. This will keep your drill straight and help you control the hopping that usually occurs as the bit tries to bite into the glass.
5. tape a shallow rubbermaid container (you can find long shallow ones at the dollar store) tape it to the spot directly under the glass to catch the water and glass debris from the drilling. The bigger the container the less likely it is to overflow if you take too long with your drilling. Make sure it sits on the styrafoam or it will tip from the weight of the water.
6. Clamp the template into place with a clamps. Use clamps with rubber feet or use a piece of wood on the back the tank so the clamping force is distributed over a large surface vs. a single point on the glass. You just need it snug so it doesnt move.
7. Make sure your drill is fully charged! Set it the drill setting. Make sure the glass bit is in nice and tight.
8. tape the back of the glass so the glass slug doesnt fall onto the floor or worse into your sump and shatter the bottom.
9. Get someone with a turkey baster to force water between your bit and the template as you drill. This will be the toughest part because you choosing to drill horizontally but as long as they squirt it in between the bit and the template you should be fine.
10. when you are done - unclamp the template and remove the slug by removing the tape. Take some sand paper and clean up the hold so its smooth. remove the rubbermaid container and use a wet dry vac to vacumm anything you missed. Remove the tape from the glass and styrafoam and use some vinegar and hot RO water on a cloth to clean up where the tape was attached - this will remove any glue chemicals. wipe down the rest of the glass as well for good measure.
11. Attach you bulk head and piping. Slowly raise the water level and check the bulk head to make sure it isnt leaking.
12. Crack open beer and take a breath
Good luck