Brett McLaughlin writes in ecoustics.com :
Given that the 990 has adjustable cross overs, how does it manage this issue?

I'm not sure if I've ever heard how this is handled exactly. I know we had some lengthy discussions on this very subject early in the 950's life (since it had a similar triple crossover). If you haven't done so already, dropping a line to Outlaw (either electronic or on the phone) might be enlightening - while they monitor the saloon, they tend to stay pretty quiet so as to let us carry out our discussions and debates on our own. Others may also know the answer this, and if you do talk to Outlaw we'd all like to hear what you find out.

I have had time to experience playing with many different crossover points with the 990, but have always ended up coming back to 80Hz across the board. It just sounds better to me. If set higher the bass seems to drown out some of the details in things and if set lower, the sound gets a little too bright at times. The only time, I don't like this is when I listen to 2-channel stereo. I wish there was a separate crossover that could be set for the mains exclusively for 2-channel modes.

I have a pair of Klispch RF-25s for fronts currently. I also have a pair of Klipsch KG-5.2s and a set of Cerwin Vega AT-15s that I could use if I wanted. I would prefer the Vegas for 2-Channel with no crossover as they will run full range. I have tried hooking these up and they sound great running full range in 2-channel mode, but I need to set the crossover back to 80Hz when using Dolby PLIIx or the bass is just too overpowering. I have tried the 5.2s with the same results as well. I ended up going back to the RF-25s and 80Hz and letting the sub kick in for 2-channel listening.

I don't know how hard this would be to do, or if it is even possible, but it would definately give me the best of both worlds.

Slightly off topic, but, this was my biggest surprise when looking into the bass management facilities. In 2-ch mode, I want exactly that 2 channels --- not 2.1-channels.

Have you tried the "2-Channel Subwoofer Offset"? The maximum is -8dB.

Have you found that to be satisfactory?

Has anyone asked for a "2-Channel Subwoofer Disable" feature in the next software release?

I use the offset as I like my bass a few dB hot for movies, so I use the offset to back it off for music. The offset feature works really well and is a big plus to have. As far as I know using "Upsample" or "Stereo" mode, if you set the speakers to large and the crossover to the lowest frequency (40Hz) you do not get the sub. However, in this configuration my fronts (Klipsch RF-25s) are too anemic and do not produce enough bass for 2-channel music. "Bypass" mode seems to kill the sub for me no matter what the crossover settings are at.

Doug makes an excellent point here - the 990 applies bass management no matter what. If your mains are effective full-range, the recommended approach would be to set them large. An alternative may be using bypass mode.

I see the multiple crossovers as added flexibility, not a problem. I have a nasty 80 hz room issue which is alleviated for the most part by adjusting the crossovers just as you describe. That way in my room, the response is closer to flat.
I design medical and consumer electronics and to me its always the same dilemma, the more adjustments you give a user, the more it can be screwed up. The item in ecoustics seems to be directed to the person who will do more damage than good, a place to start, or for the 'set it and forget it 'crowd'.
The issue isn't that THX 80hz is the answer, it is highly dependent on your room, speakers and personal preferences. I've seem too many of these "we have done the experiments and here is the answer" types of analysis and found most of them to work about 50% of the time, and not just in audio.
The fact that the 990 gives me the flexibility to make the adjustments, or not, makes it that much better.
Just my 2 cents.

In response, the Outlaws told me:
This appears to be the right thing to do.

Thanks for passing that along, quietdragon - the issue in question has been debated online for several years, so I knew that Outlaw was aware of it, but it's good to have confirmation that they took it into account properly.