Definitely do a search of posts for M3's.

I have a 1995 M3 and removed the factory amp, put in an Xtant 604X amp, a/d/s separates in the front, and JL stealthboxes in the rear.

Regarding noise, these cars are VERY noisy! If you replace the amp with an aftermarket (suggested) I suggested that you buy the best RCA's on the market (Monster Cable XLN Pro). That's what I have and they got rid of the noise (used to have crappy Phoenix Gold RCA's).

You can't just plug your rca's from the EMPEG into the dash area because there aren't any. You're gonna have to splice in RCA's into the twisted pairs in the dash but there is one for EACH speaker, so definitely out of the question. Additionally, the speaker connections are consolidated in the trunk in two plug modules (see unofficialbmw.com website for pinouts).

I ran RCA's from the front to the rear to connect to my aftermarket amp. Then ran speaker cable from my amp and spliced into all the speaker connections in the trunk. Major pain in the ass.

Good luck!
Wes
'95 M3