The Harman Kardon upgrade is a lot more serious. It has a digital amp mounted in the dash behind the speedo and beefed up speakers.
To be honest you can plug anything you like into it, it's your car
but if it's not what the connector is meant for you risk blowing things up. And I don't know your car so I can't confirm for sure. But I do know that yes, mine was in the boot (under the carpet), and that's where the CD changer is installed, and it's pre-wired into the back of the stereo. Hooking up anything other than the appropriate stacker would risk damage to the stereo. Plus if you randomly connect your amp to a connector you found in the boot there's no knowing what's going to come out of it
Have a read. Mine came with the harness and the plugs I found are the ones labelled A1 and A2. http://motoringfile.com/howto/CD%20Changer.PDF