Here's the wiring information if you want to connect your low-power linedriver to the trunk and audio input direct to the amp without running speaker wire all the way up to the front dash only to be rerouted all the way back to the amp.
First in the dash, get the standard wiring harness for the e46 and connect the 12v ignition to 12v antenna lines on the harness. Terminate the rest of the connectors.
In the trunk, remove the wiring harness from the top of the amp. The plug separates into two harnesses, one grey and one black, which look identical.
Cut the wiring and attach female RCA jacks (or just shrink-wrap tube the connections) to the jack side of the input (the leads going to the old head unit location are now useless). Attach male RCA jacks to the head unit side of the wiring. This way if you ever need to reverse your install you can just reconnect the RCA leads, plug in the old head unit, and be done. You will have 4 female and 4 male RCA jacks after this is done, one for each channel.
Pin 38 - FrontL+ (yellow/red)
Pin 30 - FrontL- (brown/orange)
Pin 37 - RearL+ (yellow/black)
Pin 29 - RearL- (brown/orange)
Pin 9 - FrontR+ (blue/red)
Pin 17 - FrontR- (brown/orange)
Pin 8 - RearR+ (blue/black)
Pin 16 - RearR- (brown-orange)
Pin 10 on the grey connector (white) is switched +12V. You can use that as an ignition lead for the carpc and matrix.
More info here: http://e46fanatics.com/faq/stereosaga.html
Do NOT use the 12v power or the ground. The factory amp system uses a floating ground, and the 12v cabling is not rated for anything beyond the factory amp it powers. I ran 12v from the battery for the carpc and the matrix audiocontrol. The SVEN ofcourse has no power.