There's nothing special about balancing with a twin max as opposed to other balancing tools. You just center a needle instead of matching heights of mercury columns. However, balancing should be the last step in a full tune up. Trying to balance your carbs when your valves are out of adjustment or your timing is off is a waste of time, and will probably make things worse.
There's lots of information on this online. For more than you ever wanted to know look here:
bmwmotorcycletech.info/synchcarbs.htm
Frank