Run the brake/stop/turn wiring from the engine compartment down in the front A post (the left front door post) behind the felt material you can see in the door post when you open the door. Run it down to under the vehicle
Run the wires in the channel in the underside of the running boards and when you get to the rear fender run the wires up and under the plastic fender liner over the rear wheel and down to the area below/behind the rear bumper. You will have to pull the plastic rivets to loosen the fender liners.
I used LED lamps and connected them directly to the MH Towing electrical connector. I mounted them right below the HHR taillights. see here to get them here http://www.tmimfg.com/
No diodes, no holes in the tail lights for extra bulbs etc.
I used their Model TM36-12R RED 12 LEDS
As to getting hoses etc. to/from the engine compartment there is a large rubber grommet high on the firewall that you can punch a hole into and run the stuff into the driver's compartment.