A method for coordinating motion between an external device and at least one mover in a linear drive system, wherein the linear drive system includes a track along which each mover travels, the method comprising the steps of: defining a first coordinate system in a motion controller, wherein the first coordinate system corresponds to one of the external device and the track; defining a second coordinate system in the motion controller, wherein the second coordinate system corresponds to one of the external device and the track and wherein each of the external device and the track are defined by one of the first and the second coordinate systems (160, 170); storing a coordinate system offset in a memory of the motion controller, wherein the coordinate system offset is an offset between the first coordinate system and the second coordinate system; receiving a coordinated motion command for the external device at the motion controller, wherein the coordinated motion command identifies the at least one mover to move in tandem with the external device; generating a first motion command at the motion controller from the coordinated motion command, wherein the first motion command defines motion for the at least one mover in the first coordinate system; generating a second motion command at the motion controller from the coordinated motion command, wherein the second motion command defines motion for the external device in the first coordinate system; generating a transformed motion command at the motion controller by transforming one of the first motion command and the second motion command to the second coordinate system in the motion controller as a function of the coordinate system offset; and controlling operation of the external device and the at least one mover as a function of the transformed motion command and of the first or second motion command that was not transformed to the second coordinate system. defining a first coordinate system in a motion controller, wherein the first coordinate system corresponds to one of the external device and the track; defining a second coordinate system in the motion controller, wherein the second coordinate system corresponds to one of the external device and the track and wherein each of the external device and the track are defined by one of the first and the second coordinate systems (160, 170); storing a coordinate system offset in a memory of the motion controller, wherein the coordinate system offset is an offset between the first coordinate system and the second coordinate system; receiving a coordinated motion command for the external device at the motion controller, wherein the coordinated motion command identifies the at least one mover to move in tandem with the external device; generating a first motion command at the motion controller from the coordinated motion command, wherein the first motion command defines motion for the at least one mover in the first coordinate system; generating a second motion command at the motion controller from the coordinated motion command, wherein the second motion command defines motion for the external device in the first coordinate system; generating a transformed motion command at the motion controller by transforming one of the first motion command and the second motion command to the second coordinate system in the motion controller as a function of the coordinate system offset; and controlling operation of the external device and the at least one mover as a function of the transformed motion command and of the first or second motion command that was not transformed to the second coordinate system.