I did it to mine, and it makes an incredible difference.
As mentioned previously elsewhere , the best way to do it is to install a line converter. Connect the converter into your audio lines BEFORE they reach the BOSE amp, then come out of the converter into your sub amp. Then, come out of the sub amp into your subwoofer.
This is easy, as the BOSE amp is mounted in the trunk of the car...so it'* very easy to get to the wires. I can send you the wiring diagram if you need it....it makes the job much easier.
Its also very easy to get power to the sub amp, because you can hook directly to your battery under the back seat.
As long as you are upgrading, you might also consider replacing the BOSE rear 6x9 speakers with something better. Again, it makes a difference.
Y2K Midnight Blue SSEi
White Cathodes in Grille/ Blue Cathodes Under Seats