A controller for an independent cart system simplifies programming and automatically adapts operation each mover travelling along a track. The controller includes a configuration table defining segments of the track, which includes a maximum velocity and/or a maximum acceleration for each mover within the segment. A motion command for a mover commands motion across multiple segments between the starting point and the ending point. As the mover travels, the controller receives a position feedback signal corresponding to the present location of the mover. The controller obtains the maximum velocity and/or maximum acceleration for the mover corresponding to the segment in which it is located. The controller automatically adjusts the speed and/or acceleration of the mover along the segment in which it is presently located. As the mover transitions between segments, the controller automatically adjusts the speed and/or acceleration according to the new segment in which the mover is located.