Axess makes a module to bypass the Bose amp. It's got all the DSP stuff on it too. Crossovers, EQ, Time Correction and a control for chime volume.
There's actually a lot of room back there, I even put spacers under the amp bolts to hold them away from the vents so it wouldn't restrict flow too much. There's also a big ass foam piece attached the back of the seat that I removed, that's just sound deadening, and it has some channels for the cabin vents. You can definetly hear them a bit more when closing the door.
I haven't done anything since I got it working, so I still have to set the amp gains, sound deaden, clean up the wiring and get a good ground.