Not how I'd set up my system, but should work just fine.

First, this Bose amp. They only offer OEM amps, AFAIK, nothing retail. Any information on this amp would be helpfull. You said 4-channel, but you have 6 speakers. How do you plan to wire it up? Maybe use the head unit for the 4 door speakers and bridge the Bose amp for the 2 6x9's?