When you decide where to drill on the glass, stay away from the edges and corners. You'll want to be at least three-quarters of an inch away from any edge to lessen the chance of cracking the entire sheet. Next you'll want to secure the glass; how you do this will depend on the shape of the glass. For example, you'll secure a glass sheet differently than a glass bottle. The key is to use something sturdy, yet soft, that can absorb the vibration. A rubber pad would work well under a glass sheet.
http://www.sgcmachinery.com/glass-cutting-machine/