I think you only need to use one of the 2 rca plugs to feed the 2 channel sub amp. Not sure if thats an option on your amp, but I know my mono amp has a mono or stereo selection option. The front/sub channel from the audigy feeds out via 2 channel mini phono to 2 channels (L for sub & R for front speakers for example, not sure if L is sub or not though). Essentially sending out a mono signal to the front speakers and mono signal to the sub.
There is also an option to output stereo sound to the 5.1 speakers in the audigy control panel somewhere (refered to as upmixing I guess?). I have read that this option resets upon restart and/or standby/hibernate. This mode should still send bass out to your front and rear speakers. It does just what a home theatre reciever would do (most retain the lower frequencies, or have an option to set speaker size).
I do not currently own an audigy NX, but had one for a few weeks and returned it because of some issues I have read about. Not sure where I am going to go next. The problem of it not keeping the setting after shutdown/standby seems really annoying to me.
Anyone with more experience, please correct me if I am wrong.