To keep the glass cool and prevent it from breaking, turn on the faucet. You want more than just a trickle but not such a heavy stream that you can't see what you're doing. Hold the bottle so the water runs over the spot you marked. Set your drill to 3/4 of its max speed and gently push it against the marked spot. To get a steady drill, first angle the drill bit so it just touches the top of the spot. Slowly angle the drill bit until it's going into the glass at a 90 degree angle, using the carved out edge as a pivot. Once you're nearly through the glass, ease up on the pressure a bit to avoid cracking or breaking the bottle. Use the drill to smooth the edges of the hole. Pour out the water and rinse the bottle several times to clean out the bits of glass. The last thing you want is to inhale glass powder, so don't rush this step. Take your 3/4" grommet and work it into the hole. Then run some water over your downstem and slide it into the grommet, carefully, so you don't push the grommet into the bottle. Insert the bowl into the stem, and you've finished!

Summary:
Get a steady stream of water over the drill spot. Start drilling slowly. Grind away sharp edges and clean out the glass. Put in the grommet, stem, and bowl.