Bob, it is customary and very helpful if you fill out a signature file (click on "Profile" in the links at the top of the page) and put in there the year and trim level of your car. There were different stereo options on different trim level Bonnevilles, so we can't really tell you much about your stock speakers unless we know which ones you have.
My own thoughts on the matter are this: If you're spending $800 to $1000 on a new entertainment system based around a carputer and power amplifier, but can't afford reasonably good speakers, I think you're putting the proverbial cart in front of the proverbial horse.
I don't want to discourage you from going forward with your carputer project, but might I ask what you're hoping to get out of it? Will you just use it for playing MP3 files and DVD movies? Because if that is the case, you might do a lot better just getting an aftermarket head unit with a motorized fold-out screen, with good integration for connecting and controlling an iPod. I just ran a quick search at Crutchfield and they have some models ranging in price from $400 to $800, that would maintain a nice clean look, without the hassle of trying to cram a computer into your car.
Unless there was some major important use or advantage to adding a carputer, I'd personally go with purpose-built products that are intended and designed for installing in cars.
Without knowing what your current speakers are, the low-end stock Bonneville speakers are pretty simple, but almost any aftermarket speaker will be higher quality. If you have a Bose premium audio system, then GM will tell you that your speakers are "matched" to the Bose amplifier with a custom active EQ circuit. I would tell you that even those tend to be pretty cheesy, and I find the Bose amplifier to be anemic. I personally would not hesitate to replace all of it with high quality aftermarket components.
97 SE, teflon wiper blades, Dunlop Sport A-2 tires, Leather steering wheel cover, Pioneer DEH-P480MP mp3 CDRW head unit, Pioneer 12-disc changer, iPod hookup, Boston Acoustic 3 way 6x9'*, Boston acoustic separates in door pods, Alpine 4 channel amp in trunk. Magnaflow dual outlet muffler and Ractive stainless tips. Autozone rice pipe and K&N 4750 intake kit. Clear corner lights. Energy Suspension end links.