I'm pretty sure you'd need to access the 990's settings menu to consistently switch between 7.1 direct and whatever other decoding you'd use for the sources. The 990 cycles through the available decoder settings making it difficult to consistently land on the desired setting. I've not been successful programing my Harmony One to access the settings menu on the 990 but I'm certainly interested if someone has been able to do so.

Alternately, if you have a 5.1 or 6.1 system I believe an Outlaw ICBM (occasionally available in the used market) can handle bass management in the situation you describe. Leave the 990 in 7.1 direct and put the ICBM in between the 990 and your amp/subwoofer. The ICBM manual is available on the Outlaw website so you can check it out to see if it would work for you. I'm using an ICBM in a stereo system as a high/low pass filter for my monitors (good to 60Hz) and a subwoofer (below 60Hz) and it works great. Lastly, Outlaw announced the ICBM-2 some time ago but it has yet to be released.