Four wires run into the control/sensor box:

White: 5V for the hobby servo

Red: 9V for the Arduino's barrel plug

Black and Green: grounds (tied together at the supply)

Three wires run out: the motor's power,  and ground lines (which simply pass through the box), and the motor logic control line.

I wrapped these wires into the configuration I wanted by clamping the far side in a vise and using a cordless drill to twist the bundle together.