To cwg25: To balance a motor the easiest method is to use a zip-tie around the motor and then run the motor with no prop. You move the zip tie around to find the position where the motor is quietest and like that you can find out where you need to stick a bit of tape to balance the motor.
Here's a video showing how to do it:
Are you talking about when you do the stick calibration? If so, it doesn't matter for the throttle as long as when the throttle is physically at zero it is zero on the assistant and likewise for maximum throttle.