I had the same complaint on my Y2K SSEi BOSE stereo...and finally got it sounding the way I wanted.... keeping most of the factory stuff.
First, before going the subwoofer route, you might first try replacing your rear 6x9 Bose speakers with something better. The BOSE units have developed a reputation for unsatisfactory sound. I put in a pair of $150 Pioneer 4-way TSA6980 '* that I found online for about $55...made a world of difference.
If you decide to go ahead and add a sub, it'* an easy job to add a second amp and a subwoofer to the stock BOSE system...at least on the 2000+ Bonnie. The result will be a much stronger bass response...and a much louder sound overall.
If you decide to add a sub and amp, you need to get power to it. Since the battery and a ground point are located under the rear seat, it'* a snap to run power into the trunk.
The BOSE amp is mounted against the left rear wall of the trunk against the back seat. It'* easy to reach, and easy to tap into the pre-amp speaker wiring to feed a sub amp. All you need is the color-code schematic that Pontiac Dad provided me (Thanks again Dad!).
Instead of tapping the pre-amp signal, you can take the "easy way out" and get your subwoofer signal directly from your rear speakers, IF your amp has a high-power input (not all do). However, since this signal has already been amplified by the BOSE amp and processed by the BOSE crossover network, you won't like the results. It'* a bit overpowering.
If you want more of a "step-by-step" on how to wire the subwoofer system, let me know and I'll be glad to provide.
Y2K Midnight Blue SSEi
White Cathodes in Grille/ Blue Cathodes Under Seats