No alternator whine for me except when I switch to the tuner. I had to use the harness extender that came with it so I'm betting that is the culprit. It is very, very faint. I only hear it when listening to the classical and soft rock stations here.

The MC4000M is mounted across the back seat (I don't have fold down seats). Fits perfectly with a couple of inches on each side for hookups. 4 gauge power runs thru a fuse to the battery (I'm so glad BMW put the battery in the trunk!) and a 4 gauge wire runs down the driver's side behind that plastic, removable floor panel. Below the taillight is a large bolt that is attached to the rear bumper. That's where I grounded the amp.

FWIW, I had a Sony MoblieES system before the Empeg with the same amp. Never had any alternator whine issues with this setup. Oh - my RCA cables run down the middle of the car, under the center console. I also have a 1.5 farad cap hooked up to the amp.