yes it does. the factory amplifier separates the signal. all it gets are LEFT and RIGHT audio inputs.

if i understand what you're asking, it would involve running wires from each individual speaker location back to the factory head unit. furthermore, it wouldn't work because you would need a headunit with 6 amplified channels. even if you ran the subs off the rear speaker outputs, you would need to filter out anything above 100-120Hz, which the head unit could not do (most likely).