@eminus you can do the following:
In the config.g file, use the M584 command to configure 6 axes, one for each motor. I suggest you use X Y Z U V W. Implement some sort of homing mechanism so that you can move each joint to a known position. You can use microswitches, optical or Hall sensors, or (if the mechanics is tough enough) motor stall detection. After homing all 6 joints, send G1 commands to the Duet from the Pi to control the joints.