I've got an E36 M3, I drilled a hole in the spare tire well and grounded with a bolt (after scraping away paint till I got to clear metal).
I too mounted my amp upside down under the rear deck.
At first I had noise, when my amp was mounted directly to the metal
Then I switched amps (Phoenix Gold --> Xtant) and mounted the amp on a board which mounted under the rear deck. The noise went away.
I frequented the CarSound discussion boards and made some muting plugs (cut an RCA cable, and twist both the conductors together...essentially shorting out the plug). I then put the plugs in the connectors on the amp. If you still have noise the noise is either coming from the amp or the speaker cables. If you have no noise your amp (and your ground) is clean.
Then plug the shorting plugs into the RCA cables in the front of your car (with some male-male adaptors) and if you have noise there but no noise from the previous test it is your RCA's that are bringing in the noise.
The best RCA cables made (quietest) are the new ones from Monster Cable called XLN-Pro, designed by David Navone and Richard Clark. If you want a set cheap, call David Navone (www.davidnavone.com) and beg a plead for a set.
Good luck!!!