Firstly, you'll need patience (and be prepared to break a few bottles!) Then rough up the surface where you want to drill with emery paper. (Helps to stop the drill slipping when you start). Tape over the point where you want to drill also with masking tape - it will also help to stop the drill slipping and contain broken glass when it all goes wrong. Place the bottle in a vise. Use a drill for metal, make sure it is sharp. Be prepared to blunt a few drills. You'll need patience (I know I already said that).
Personally, I've never done this, but if you search with your question
How to drill a hole or two in the neck of a glass bottle
you will get a significant amount of references.
Heat the glass to white hot ... Then just poke the drill bit through slowly.