See
http://empeg.comms.net/php/showthreaded.php?Cat=&Board=install&Number=90443 for a discussion on this subject.
I had to custom splice molex connectors to be 'plug and play' with the connectors in the trunk just in case I wanted to put my old amp back in.
My system:
-Rio Car (of course!)
-a/d/s 345is Separates (front)
-JL Audio 8" stealthboxes for BMW M3 (rear)
-Xtant 604x 4 Channel Amp (mounted upside down under the rear deck)
-Monster Cable XLN Pro RCA Cables (THE best!!!)
The only non-factory wiring I am using is the RCA from the EMPEG to the AMP (Monster Cable XLN Pro) and the power/ground to the amp. All other wiring is tapped in via the factory connectors in the trunk.
You may also want to read the E36 Stereo pages at
http://www.geocities.com/MotorCity/Boulevard/3287/car_audio/stereo_upgrade.html and
http://www.unofficialbmw.com/e36/stereo/
You may find noise to be a particularly persistent problem in BMW's....the Monster Cable XLN Pro cables are your best bet for reducing/eliminating noise. Also, don't mount your amp directly to any metal as it could introduce ground loop noise.
Good luck!!
Wes
'95 M3