Yeah.. the wire would go where the jumper block gets plugged in. I would put a spade connector on each end of a short piece of wire and plug those in.
The green connectors would be connected with the toggle switch, since you can't drive the car with them hooked together (but they have to be plugged in to write to the ECU). Although I was thinking you said your car doesn't have the green connectors because a previous owner had cut the wires?