Hi Alex,
Driving a motor like this with the PDM is not the easiest thing to do, as the PDM is designed to run a device that works in a single direction, such as fuel pumps and coolant fans. What you need to do is to be able to drive a single motor in both directions using only two wires, as per the diagram below.

- Single Motor both directions.PNG (22.83 KiB) Viewed 11673 times
As the PDM only drives the outputs High Side, and doesn't have the ability to sink voltages to ground, you need to find a way to ground the opposing pin when the the motor is driven. A way that this could be done is using the MoTeC DHB (Dual Half Bridge) in a full bridge manner. This will allow for one side of the motor to be driven whilst the other side is sunk, and then change the direction of travelled by swapping the Pin status. If you used a DHB, the PDM can be used to supply power to the DHB, and then the window switches would be wired directly into the DNB to control the direction of the motor.
You will not have any travel limitation with this system, as there is no easy way to integrate the limit switches into the operation of the controller.