I just wired my limited roadster for an amp in the back. I chose to run the wiring under the center console instead of under the carpet. Its much easier to route the wiring and the RCA cable and remote turn on wire can be quite a bit shorter. There is also the benefit of never having foot pressure on the cables which can cause breakage.
As far as routing through the bulkhead, just follow the rest of the wiring. Plenty of space in there for more cabling. I have a sirius cable, a fat Monster RCA cable, 8ga power wire and remote turn on wire running through the opening and there is plenty of room for more.