I played a few DVDs today and found that the best setting for movies (DD/DTS) was:
Fronts: Small, 60Hz
Center: Small, 100Hz
Surround L/R: Small 100Hz
Sub: Yes

That way all the bass below the crossover levels + LFE (.1) was sent to the sub.
One thing weird I notice that was when changing between a DD track and DTS track (on the same movie), there was more pronounced bass on the DTS. Not sure why.

I then left the above settings the same and played a few CDs using the Digital Coax RCA from my Adcom player connected directly to the 990 in "upsample" mode.
It sounded good, but not great. The bass was lacking (2CH bass ofset was at 0dB), so I went in and changed the Fronts from Small to Large and changed to Sub to LFE+L/R.
That fixed the problem. I got full range bass to the fronts and L/R bass to the sub.

On a some of the CDs, I could "feel" an extremely low frequency coming from the sub.
I tested this by playing a CD track that just had 1 person singing. I could not hear, but could feel the sound waves coming out of the sub.
I stuck my hand on the woofer and it was viberating very slowly.
Since this was only on a couple CDs, I guess this would be low frquency jitter that was durring the recording process?