About a week ago I found time to start listening to my new B&W 804S and HTM3S speakers and have been trying out different modes and crossover settings on the 990.
As of now, I've found that setting the speakers to "Small", with a L/R crossover at 40Hz and Center at 60Hz produce the best results. I've also found that I have to use "Bypass" mode when listening to CDs (digital rca input), as "Upsample" now sounds too harsh in the upper frequencies.

If I were to use an External DAC (such as the VDA-2), I'd have to connect my rca digital cable to it, and then use rca analog cables to the 990. In doing so, if the 990 was in "Bypass" mode, according to the Analog Bass Matrix, the L/R Speakers and Sub would get full range sound and not use the crossover.
http://www.outlawaudio.com/support/990_analog_bm.html
If I'm using Bypass mode now with digital input and fronts set to small, it will use the crossover and send bass to the sub, but if I use analog inputs, it sends full-range sound to the fronts and sub?
This makes no sense to me.
How then can you use an external DAC and still use the 990s crossover?
According the bass matrix, I'd have to use Stereo, Upsample, or Dolby.