Ok, first off you don't need to replace your speakers in your car. The ones that you have will work just fine. There are a couple of different ways of doing it however. The easiest way would be to buy what is called an amp integrator. Basicly what it does is takes the wattage that the aftermarket stereo puts out and converts it to a low level voltage signal that the Mach amp can understand. When you do this it is a good idea to put a 4.7Kohm resistor on the remote turn on wire for the factory amps to keep them from popping, although I have done several of these cars and not all of them will pop when turned on and off. Another way you could do it is to take a set of RCA's and cut the ends off of them, leaving about 3 inches of wire to work with on both ends. Strip them back and use the wires on those to wire to the aftermarket harness that plugs into your factory wiring. Then just plug your RCA's into the back of the headunit and you are good to go. And then you could also just run new speaker wire to the factory amps in the back and unplug the plugs from them and take the time to figure out which wires go to which speaker and hook the wires that you ran accordingly. The final way would be to leave it hooked up the way it is, take your door panels off and run wires from the tweeters to the woofers in the doors, and then take the Mach 460 amp rack down and run wires from the tweeters there to the woofers in the back, and then you should have perfect sound once again.With that being said.......It sounds to me like the Best Buy that you had install you radio just unplugged the bypass harness from behind the dash and used it to wire up your stereo. The only problem with doing this is that plug is only for the Tweeter amplifier behind the dash and thats why the speakers in the bottom of the door are not working. I know this is a lot of info but I hope it helps. By the way I am an installer at BEST BUY, so I hope you don't think I am a dumb ass just because I work at Best Buy and not Curcuit City. Theres nothing that pisses me off more than one shop talking **** about another shop, just my .02.