What do you mean when you say "multitrack sources" in your subject?

Unless something on your PC is encoding to Dolby Digital or DTS in realtime, you will only be outputting PCM from the PC over a digital link. I don't believe the Audigy has DDL (Dolby Digital Live!).

It shouldn't stop you from using Dolby Pro Logic II in a 5.1 system (or IIx in a 7.1 system) to decode matrixed surround (Winamp Surround Edition does - I'm not familiar with it). What happens if you tap the Surround mode button, and then up or down arrows on the front of the 990? That should let you cycle through surround modes while you have music playing.

If you're trying to get discrete 5.1 output from your PC into your 990, you'll need to do it with analog I'm afraid, and go into the 7.1 direct inputs.