Mine works the same as Shanes. IO card to faders on a Yamaha mixer, system sound to faders on the Yamaha mixer, from the PC output jack. The two are independant.
If you are using Avid through the system sound, i would assume it would take over control and not relinquish it until you exit Avid, or turn off the hardware tool on the timeline. (if that works with system hardware). This is how it works on an I/O box. Once Avid takes control, if i play a quicktime out through Switch, i get no audio or video on my output card until I turn off Avid.
Glenn