Hooking up two sets of speakers.... doesn't tell us too much. Most modern motherboards have 8 channels of audio on four jacks; Left/Right, Center/Subwoofer, RearLeft/Rear RIght, SideLeft/SideRight...... What motherboard do you have?
So, you can hook up three pairs of speaker, a center channel speaker, and a subwoofer. If you're looking for a surround setup just select 5.1 (use L/R & RL/RR outputs) or 7.1 (L/R, RL/RR, SL/SR outputs) be sure to hook up a single speaker to C for Center too. And, a subwoofer if you have one.