Hrmmm. Where to begin?

Let's start with your head unit. Bose isn't bose without the matching head unit. They have built in EQ curves that change with the volume knob. Essentially, they add their own low level signal processor specific to the vehicle installation. So you should do everything you can to maintain that.

HOWEVER!!! Most people never notice a difference when they swap head units anyways It's generally accepted that if it sounds different it MUST be better

Therefore, if you swap out the head unit and utilize their $4 speakers with good results...then just keep on truckin!

So let's figure out the basic install first and then we can move into disc changers, etc.