What is the best way to charge
The battery cycle is exactly what it says, a cycle. This means that it will count charge and discharge cycles as a whole.

An couple of apple genius guys I talk to recommend at least 2 charge cycles per month, and trying not to leave it plugged in at all times will keep it relatively healthy.

You don't need to completely drain a battery before you charge it either, but the more complete the cycles are, the better accuracy will be on the battery meter.

It's a hotly debated subject, but apple do have information on their website.

http://www.apple.com/batteries/notebooks.html