As long as there is only one amplifier on the other end it won't matter. If you use both sets of wire you will double (depending on exactly what was run behind the wall) the AWG of teh wire (better deffinition in the bass). Take off the wallplates before to ensure that all wires match up on both ends to ensure you don't blow anything up. A multi-meter can idetify any possible shorts behind the wall too.
Good luck!