An improved system and method for coordinating motion between an external device and independent movers traveling along a linear drive system includes a motion controller generating motion commands for both the external device and for each of the independent movers. Coordinate systems are defined in the motion controller that correspond to a track along which each of the independent movers travels and to the external device. An offset between the coordinate systems is also defined. The motion controller receives a command for coordinated motion and generates motion commands for the independent mover and the external device in one coordinate system to achieve the commanded coordinated motion. The motion command that corresponds to the coordinate system in which the motion commands are generated are transmitted directly, and the motion command associated with the second coordinate system is first transformed to the second coordinate system using the offset.