The "digital" option will convert the analog to digital and apply the quadruple crossover settings. I don't think you can apply any other processing (such as PLIIx), but that's about it. I'm not sure about where small center and surround data would go when the mains are large and the sub's enabled - if nothing else, Outlaw support should be able to get you an answer.

The 990 lacks the 970's switch - if all speakers are set to large it acts the same as the "bypass" option on the 970, but if some or all speakers are small it acts the same as the "digital" option.