I'm posting from the road tonight (about 300 miles from home, checking work e-mail in a college library), so I'll be brief...
Sluggo's right that for HD, Dolby Digital is the standard audio format. For regular digital cable, you'll get a mix - analog stations will be converted to PCM stereo (if your box is well behaved, as I think most are these days) while the digital channels will be either PCM or Dolby 2.0.
The 990 (and any other surround processor) is able to recognize and identify any incoming signal format and decode it accordingly. Just trust the 990, and it'll take care of you.