To be honest I'm not sure because I havent worked with the Bose system you are describing. I have two theories tho.
1.) you need the Bose integration harness
Or
2.) You just color match wires like normal and the one set of wires it has the rear split at the amp that contains all the crossovers and stuff. Because I believe those 5 1/4's and 6x9's act as speakers and separate subs.
Is there more speaker wires at the head unit than just front and rear (4 sets of wires)?