That's a tough one . . E39 right? They're supposed to be similar to E36 systems, of which there are 2 different setups: a 6 and a 10 speaker setup. Try to get acess to a Bentley manual, they have excellent stereo wiring diagrams at the back of the book. In any case, you have to pull the signal from the output of the radio before it enters the stock amp, since the amp also has the crossovers built in. However, your radio may not be able to handle splitting its outputs to both the stock speakers
and the new amp. Additionally, your new amp has to be able to accept speaker lever inputs.
What people normally do is replace the stock amp altogether with a multichannel amp, or replace the head unit with one that has both speaker outs and RCA line level outs, neither of which is your situation. Sorry I can't be of more help
