Cool cheers guys.
For now I'll probably just run the Bose speakers off my Alpine iDA-X303 and leave the tiny amp running the sub for now and see if it's any better. So does that Bose amp run all the speakers in the default setup?
My old setup was with Vibe components in the front, with the tweeter mounted in the a-frame factory locations and the woofers in the doors, then kenwood 6x9's on the parcel shelf and a 12" Fli trap sub in the boot with 1000watt amp running it. Sounded great! The headunit has a built in cross-over too so I can isolate the sub freaquencies from the speakers and send them to the sub. The Bose unit doesn't even have a sub volume level!
I was hoping to be able to run the existing sub via the sub pre out on my head unit, but I'm not sure what the Bose amp inputs are or if it even has pre in's, anyone know?