I read through the instructions of the Diddyborg, I grabbed the below image from their website.
In the bottom right, you can see that the reverse motor controller users two sets of comms cable and users the top 6 GPIO pins.
On the BerryGPS-IMU, we break these pins out for you to use. You can then connect the BerryGPS-IMU to the GPIO on the Raspberry Pi, and the comms cables from the motor controller can connect to the pins broken out below.
Take note, we removed the extra 5v pin to save space. so you may need to modify one of your cables.
Below i list the first 10 GPIO on the Pi, and on the right are the pins broken out on the BerryGPS-IMU to compare