Thanks for that John,
After reading your comments I went back and looked again and figured out that I missed the part where this was being soldered onto the shield plugs placed on the arduino and not soldered directly to the board as I had thought. ( Arduino motor/stepper/servo control - Solder it! )
So in order to stack this board I should solder on headers instead of directly to the board as shown and avoid reusing any pins that are used by the motor shield?