I have new 970 and use 5 channel stereo for music.
In that mode I have noticed I need to turn down the LFE signal to the sub to blend in properly with the rest of my speakers. When watching DVD's or TV in one of the Dolby modes, will I need to increase the volume of the sub manually to adjust for the change from 5 channel stereo and then manually turn it back down again when I switch back to 5 channel stereo for music?

5 Stereo and 7 Stereo will be more bass heavy because of the way the signal steering takes place. It will also be louder at a given volume setting, although the overall effect is not quite as pronounced as for the subwoofer. You are copying left channel (without any decrease in signal level) to at least one extra speaker, copying right channel to at least one extra speaker, and copying a mix of the two to the center. Then you are applying the normal bass management on all of those speakers, such that you get two and a half copies of the bass from each of the two original channels.

So, does it follow that I should expect to have to turn up the sub when I watch tv and movies in dolby mode to achieve the right balance? Or, will different audio inputs retain custom callibration settings?

The normal channel calibration settings, the levels that establish output ratios between the various channel outputs, are global and remain the same regardless of the source and mode, except for one optional item, the 2-channel stereo subwoofer offset. See page 32 of the 52-page Outlaw 990 manual, also available on the Outlaw web site.

http://pdf.outlawaudio.com/outlaw/docs/990manual.pdf

Because the 5-stereo and 7-stereo modes copy signals from the two channel stereo mode, I am unsure if the two-channel offset may have an effect, intended or otherwise, when in 5-stereo or 7-stereo mode. I'm not at home to check this, but you could go into 5-stero mode and see if wildly changing the two-channel stereo offset results in any noticable changes to the subwoofer's output.

I was just wondering the same thing myself, bestbang4thebuck. I don't think that the two-channel sub offset (which is also availableon John's 970) applies in this mode, but I wouldn't swear to it. Certainly worth a try. A quick and easy test for it might be to use my DTD or some other disc with a low frequency test tone contained in the front channels only with the sub offset at 0dB and at -10dB.