Abstract: Systems and methods of associating components of a surgical instrument for navigation-assisted surgery, and controlling the surgical instruments. A first association is generated between the end effector and the navigation array from an input based on an arrangement of tracking elements of the navigation array, and an identification signal. A second association is generated between a power source and the navigation array from a battery signal wirelessly transmitted from the power source that is indicative of current being drawn on the power source. The power source may be controlled based on a position and/or an orientation of the end effector and a pose of a patient tracker. Should the position of the end effector cross a predefined virtual boundary, a control signal wirelessly transmitted to the power source may alter the current being supplied to a motor. An inertial sensor may provide a movement signal used for generating an association.