The rear 6x9s have two coils. One that plays a full range directly from the radio and the other that plays the low frequencies from the amplifier. The amplifier has 4 inputs, one from each channel from the radio, and two outputs that are somewhat controled with the gain slider.
By connecting the aftermarket speakers as described above, they will play the full range of frequencies from the radio but the gain slider will have no effect. If you connected the speakers to the other wires (the striped ones) they will only play the bass from the amplifier but can be controled with the gain slider.
I suppose you could hook them up the other way but personally I woulf prefer the rear channels to be full range. Some members have used the unused wires as inputs to an aftermarket amplifier to run a sub box or other subwoofer application. This is pretty slick as you will have considerably more bass than stock and still have the gain control.