From what I understand, if you add the 6-disc changer, it sits in the 'storage' space below the main radio, but it does use the main controls, and displays on the MFD. It does *NOT* take over the existing CD slot. (Meaning you have a single CD slot where it is stock, and a 6-disc slot just underneath, hidden behind the smoked plastic door.)
Someone will correct me if my beliefs are wrong, though. (People always try to correct my beliefs. )
I had the changer added to my package #7. It sits below the standard (non-JBL) CD radio in the 'pocket' there. Essentially I now have a 7-CD system: the single CD basic stereo and the 6-disc changer. ALL functions are displayed on the MFD as well as the steering wheel functions can control the changer. The only buttons on the changer itself are to load and eject each disc. I find the changer handy since it's right up front, no cartridges to fumble with. And it does a full 6-disc random which is WAY cool. With the basic (non-JBL) system, my dealer installed it when it came in. The JBL system already has a 6-disc changer/cassette unit. The pocket below the JBL system would be for storage then. Not sure if you could add the changer to such a system (for a 12 disc system) Hope this helps. Love my Prius!