Is this a 2 channel or 4 channel amp.
If it's twin channel is may be trimode compatible, where you wire the 6x9's or what ever to the appropriate channels i.e left and right, then the sub is wired to negative left and positive right.
Above is going from memory so may be wrong, if so can someone correct.
If it's a 4 channlel amp the the 6x9's would be wired to the front outputs and the sub would be bridged across the rear outputs, similar setup for sub as described above.
Hope that helps.