I finally finished my brake controller installation. Like Midnight Rider, I brought the wires from the 7-pin connector through a grommet in the spare tire well, routed it under the door sill trim, and through the firewall. To more easily get through the large rubber firewall grommet, I enlarged the hole at the nipple on the engine compartment side of the grommet using a Dremel tool and a grinder. The circuit breakers were installed under the hood next to the rubber trim as Midnight Rider described.
The Redarc Tow-Pro Elite controller was mounted on an empty bracket I found under the dash. The controller was mounted with nuts and bolts, Scotch mounting tape, and a zip tie. Overkill - but I'm confident that thing won't be moving.
On the right you can see the brake switch. I identified the wire which only has power when the brakes are applied via the brake pedal, and tapped into it with a splice connector.
As others have commented, the trailer brakes will be activated by the brake pedal but not when the brakes are activated by the cruise control.
I chose the Redarc brake controller because the only part of the controller that is visible inside the car is an inconspicuous knob. I installed it below the switches on the left side of the dash. I had to modify the back side of the dash panel a bit for the controller's switch module to fit.
A press on the Redarc control knob will apply the manual override brake to the trailer. The knob is easy to see and reach and doesn't affect leg room like many other brake controllers on the market.
My CX-9 is trailer ready!