I kept the 6 pin connection in the engine bay but tucked it away up and out of sight. this way I could disconnect and remove, if something ever happened to the fitech, without the need to pass the connection through the aluminum. I then have the wires that are from the other side of the 6 pin plug which go to the fuel pump relay, fan control, ignition, etc; integrated into a split loom that I put through the pass-through hole which is shared with the rear harness. Then those particular wires are separated to their needed location within the ds footbox area.
The controller plug ins hang loose under the air cleaner. If i ever need to run and drive it while checking the controller, I can close the hood over the cable and keep my eye on the screen. But that has never come up. I keep the controller in a box in the trunk.