FAUguy,
So .... how does it sound? what is the 411?

So far I've only had a few hours today to try it out.

First, I decided NOT to run the Auto Setup.
I went into the settings and told it how far away the speakers were,
what the speaker size was, and crossover settings.
This is what I had:
Front L/R: Large, 40Hz (B&W DM603)
Center: Small, 60Hz (B&W CC6 S2)
Surround L/R: Small, 100Hz (B&W DS6).
All were at 0dB.

I listened to everything for a while and it sounded a bit out-of-balance, so I tried the Auto Setup.
It changed distance measurements for the L/R/C speakers. It said the sub was 16ft and the L/R were 12ft, but the sub is sitting next to the L speaker.
It changed the front L/R speakers from Large to Small. It kept the Center and Surround L/R small.
It said the front L/R were 0db, Center +1db, Surround L/R +3db, and Sub -8db (volume knob was at 5).
It did not change the crossover values (front 40, center 60, surround 100)

I listened to some passages from a few DVDs, and it sounded better, but something was missing.
There wasn't enough bass coming from the from L/R speakers.
So I went back into the settings and changed them from Small, to Large.
This made an improvement, so I then changed the center from Small to Large.
That made a difference too.

When playing a CD, I use an Adcom CD player output via Digital RCA (MIT Reference Digital cable) to a CalAudio Sigma2 DAC.
I would keep the 990 in Bypass mode since it sounded cleaner.
I then decided to take the Sigma2 DAC out of the loop, and connected the Digital out of the CD player directly to the 990.
I put the 990 in Upsample mode. It sounded just as good, if not slightly better. I would change between Stereo and Upsample
modes, and Upsample does improve the sound quality.
But it's hard to tell what sounds better: Using the Sigma2 DAC and 990 in Bypass, or just 990 in Upsample.
One thing that did make a difference was to have the sub on as well (in LFE+L/R mode) when playing a CD.
It did not make the bass overpowerfull, but did make it stand out more (most noticeable when playing the Saint-Saens Organ Symphony No3. You can "feel" the low pedal tones).

Overall, in the few hours that I've had to use it, I am quite happy with the results.
If I had an extra $1K, I would of got the 7700 amp, but the 7125 sounds as good or better as the Adcom amp I had.
I still need to look and see if I can find two Rear Surround speakers that would be able to ceiling mount because there is no back wall (open stairway).
I LFM-1Plus is gives more than enough bass for my room (using it in bass extension mode 20Hz).
I might also look into buying a new remote. I think I liked the remote with the 950 better. The blue backlight on the 990 remote is bright and distracting when watching a movie in a dark room.

I'm sure I'll have more to say after I've tried it for a few more days.

Edit: I tried the AutoSetup a few other times tonight to see if it would give the same results. One thing I noticed is that it DOES NOT change the crossover settings. If I have all the crossover setting at 200Hz, and run the AutoSetup, it is kept at 200Hz. No matter what I set them as, the AutoSetup does not change it.
Is this correct?
I thought the part of the AutoSetup was to determin the crossover settings for each speaker so it works best with the sub.

FAUguy,

Isn't 40 Hz a little low to run the crossover for the fronts? The B&W's have their +- 3 db level at 44 Khz, so you're creating a fairly large bass dip between 40 and 50 Hz or so that the sub could easily cover. It would also take off a lot of strain on the 603's to set the crossover at 60 or even 80 Hz.

I looked at the PDF files for all my speakers today.
It says the DM603 (front L/R) are 47Hz to 20kHz +/- 3dB.
CC6 S2 (center) is 78Hz to 20kHz +/- 3dB.
DS6 (L/R Surround) is 85Hz to 8kHz +/- 3dB.

I have the crossover on the fronts at 40, center at 80, and surrounds at 100 (80 makes to much bass distortion on the DS6).

The reason I had the crossover at 40 is because when I listen to 2CH music CDs, I like to get full front speaker sound. Otherwise, if I had the crossover at 60 or 80, then I would be missing the lower range.

Advice?

I would say that if you wanted to drive your fronts in full range, to use the bypass mode. However, bass that low (40-60 range) really shouldn't be too directional at all, so at least to me, I'd say you would be better off setting the crossover to 60 or 80 on the fronts, routing that to the sub, and it should fill that bass dip and probably let the fronts perform better.

I'd also consider trying out 100 Hz for the center, since the -3 db is so close to the 80 Hz crossover, the rears seem good. No real way to be sure unless you test it out, though, and decide what sounds best to you.

I'm going to agree with smackrabbit here (oh, and welcome to the forum, smackrabbit!). I used to run my mains crossed over at 40hz when I had an SVS sub for the very reason you mention (music listening), but with my LFM-1 I was able to bump that up to 60hz and have the sub and speakers integrate quite transparently. You might want to give it a try and see what you think. I'd also suggest trying 100Hz for the center channel to see how it works for you.

Ok, so if I'm understanding correctly...

[DD or DTS]

1)When all speakers are set to Small and the crossovers would be front 60, center 100, and surround 100. All bass below the crossover points + LFE will be sent to the sub.

2) If front L/R are set to Large, center Small, and surround Small, then the sub would get the bass from only the center+surround+LFE. The front speakers would get all the bass regardless of the crossover setting at 60.

Between these two choices, it would probably be best to have all speakers set to Small and have the sub handel all the bass below the crossover points when using DD or DTS.

However, when using a CD player with Digital out to the 990, should I keep the settings the same and use "Upsample"....Or I could change the fronts to Lage and sub to LFE+L/R. This way the fronts would get full range sound and sub would get low L+R bass (since there's no LFE on a CD).

What do you think?

Myself, I would keep the settings the same and experiment with 60 Hz and 80 Hz crossovers. From around 80-120 Hz and below, bass is non-directional, so to me you are getting the most out of your speakers (and I am from mine, which are around the same size as yours and are +-3 db at 48 db) since they won't strain, and the sub can easily handle bass up to 80 Hz without breaking a sweat.

It all comes down to personal taste, I just think that the current settings with the 40 Hz crossover was just leaving too large a hole there in the bass, and worry that doing Large+LFE will wind up with too much bass. If everything is calibrated right, it should be nice and smooth.

You've got the bass management figured correctly (if it helps keep track of it for other configurations, I've got a bass management diagram on my firmware updates page). I'd recommend leave the mains small (60Hz crossover) and playing with "upsample" in stereo mode for CD listening. If you do decide to go with large, you'll probably want to avoid the "LFE+L/R" mode because you'll still get the extra bass you didn't like before.

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?