A method of aligning a door operating system for operating an upwardly acting door including an operator that directly interrelates with a counterbalance assembly in the door operating system to move the door, where the operator is at least partially supported on the counterbalance assembly, loosely attaching the operator to a header adjacent the door, and, moving the door from a closed position to an open position and returning the door to the closed position to achieve alignment. Once aligned, the operator is securely attached to the header to maintain the system's alignment.