1. run wires directly to speakers themselves, from receiver.
2. I assume your sub has a low level input, an rca jack, and it might be called something like LFE, maybe not, but you want to connect to the RCA style input from the subwoofer/lfe low level output on the receiver.
3. set all speakers to "small", try 100-120hz, since your speakers are essentially cubes.
the way you have it now basically uses the subwoofer for the "front channels". It's taking front channels duties, and simply splitting them with the fronts. Well, this is a very watered down explanation, so that I don't freak you out... but that's the essence of it.