Before fitting the side covers to the flap actuator frame I decided to make up a simple little angle bracket to help with the wiring. See pictures below.
I fitted the flap motor wires off into a male molex plug, and mounted the matching female socket in the little piece of angle.
I also fitted a couple small wiring bushes in case I want to run something through this section (eg; headset wires).
I added a simple bracket to hold a flush mount molex plug, and a couple wiring bushes