For my set-up, I kept the bose HU too. MTX has a new line of amps that can use speaker level inputs as a source...so I disconnected the rear midbass speakers from the back seat, and soldered the RCA jacks on. Sounds great, and I don't need the JL's cleansweep, or audio controls' A6 processor! But, this was to add a subwoofer to the car, not to replace the bose speakers (which sound ok...).
All in all the cost was 2k for the amp, 2 MTX 10s, and fabrication/install/dynomat. This way, I can enjoy better sound now, and upgrade the rest later (another 2k...). Here's a link to my setup:
zerothread/173934