Piggybacking off what brandes.cm posted, you will have to find the factory amp and bypass the amp's speaker level inputs/outputs. Give yourself enough room when you clip the wires to be able to reconnect later on. I just did one in my cousin's '01 tahoe and his was located in the passenger floor board close to the underside of the dash. This will allow the power to jump from your source to the speakers without being blocked by the factory amp. I did it in my Acura Legend years ago without any problems, too. Should you decide to convert back to the factory amp later on, just reconnect to the factory plugs on either side of the bose amp that were left over, plug in the factory deck, and you're on your way. Hope this helps.
1998 BMW 540i
Headunit: Stock DSP; Hifonics MX-1
Front Stage: Cerwin Vega 5.25's
Rear Stage: OEM 5.25's
Sub: RE Audio SX 10.4
Amps: Rockford 400.4 & bd1000