The point of calibration is to set the servo such that it doesn't rotate when at the centered position (127 on a 0 to 255 bit range, or 1500µs). That way, you always know what value to send via code to stop the servo.
So put code into the arduino that would center an unmodified servo. With this signal being sent to your modified servo, it will rotate if the potentiometer is not in the centered position. The servo uses the potentiometer to judge the position.
Hopefully that explains it well enough. I could explain more in depth how the potentiometer position is "judged", but that's not needed at this point, I think.