Depending on how you wire your motors and assuming the motors are essentially identical, you should not need to adjust them independently. Are you trying to remove a beat pattern at a particular throttle setting? Are you using a single controller, or one for each motor? Due to slight variations in motors, prop loads, throttle curves, etc. it can be virtually impossible to perfectly sync both motors at all throttle settings. If you have a separate control for each motor, then the master/slave program will probably work for what you want... but it seems unnecessary to me. If you want to steer or adjust trim using differential thrust... that's a different matter.

-David