Glass can be a little complicated when photographing because it takes on the colour of your background and therefore you can easily lose the edges of your object(s). The easiest way to deal with this is to place reflector of the opposite colour as your background on either side of your object.
For example, if you are shooting on a white background, place black reflectors (or pieces of paper) just outside of your frame. This will make the edges distinguishable from the actual background as they will now reflect black.
The above photo has a reflector on the left side of the image and above it as well to reduce glare from the soft boxes that are lighting the subject. Another trick that helps is to put something in the glass itself (e.g. coloured water).
The above photo has coloured water in the glasses and black cards on either side of the image to help with the stems of the glasses.
When it comes right down to it, it is a process of trial and error. Eventually you will be able to determine a better starting point and your sessions will generate less error-filled shots.