I got the wiring diagram and noticed that the sub woofer is connected to power. Does it have its own amp? It seems like the "bose speaker amp" has a "sub output" going to the sub harness which also takes a constant and switched 12v. what is that thing? If I replace the main amp with a 5 channel amp, can I just connect the 5th channel to the "sub output line"?

 

I think you are correct about the main amp, if you look at the sub connection you will see that it is connected to power and remote-on as well. I think that means another amp. I think the reason why we are not getting an answer is that some people connected new subs so they didn't care, others replaced the head units but kept the amp (they didn't care either).