XP, Vista or Win7? From what I have read vista and 7 changed something with the audio portion of the OS. What is it, may be the audio engine or something (someone posted it on here or the centrafuse forums). Long story short 3.1 for me at least wont show the front or back speakers when I have my speakers setup in quadraphonic, 4.1, 5.1 6.1 mode. When I ran XP, Centrafuse could see how I had my speakers setup. Split your Left and right (Green jack) to a 4 channel amp. This is my current setup:
Left/right (green) 3.5 jack to a 4 channel amp. Line out on 4 channel amp to Sub. Sub controlled with a aux bass knob.
Hope this helps PM if you have any questions?