As far as I'm aware, you won't stand a chance using the standard wiring loom, the installers had to run power/phonos back through there.
Bear in mind, the bose sub is a tiny thin pos. The boot is the best location for a sub, not where the bose sub goes anyways (got a jl 10w3v3 in the bose sub compartment and stuff around it rattles, a fair bit). I also don't see why you'd want to replace it with a free air sub?