Always wear protective eye gear and always drill in water. Your lungs do not like to breathe glass dust. Also, friction of the drill on the glass causes heat and thus cracking.
1. Use Diamond Core Drill Bits. I have tried bargain bits and they are no bargain. My favorite come from Rio Grande.
2. Mark glass with a sharpie
3. I use a take out container with a block of wood set in it. I invert the lid and place on top. The lid creates a small pool for water. The block underneath acts as a hard surface to stabilize your glass.
What's with the duct tape? You will eventually drill through the lid and need to 'reupholster' it so that the water does not leak.
You could also set a piece of wood in a dish of water but the wood floats leaving you to hold down both the glass and wood.
4. SLOW and STEADY! Let the drill do the work. Lower it for a few seconds. Then raise it to clean the debris. Once your hole is almost through. Flip the glass and drill from the other side. This helps avoid cracking and crazing.
5. Keep a full pitcher of ice water and a big empty bowl handy. Your water will cloud up and need frequent changes.
6. Cracks happen sometimes. I play by a rule "three cracks in a row - time to quit."
SORRY THE PHOTOS ARE ALL MIXED UP. TRIED AND TRIED TO ALIGN THEM.