Roger, i don't see a problem with doing what you want to do. It would be nice to have a processor with different bass settings for your different modes ( stereo vs ht, etc..), wouldn't it ? Unless you have the capablility to do such or have dual subwoofer output jacks, you'll have to split the signal coming out of the preamp with a Y cord or adapter and run seperate lines. Outside of having the seperate settings, the only alternative that i see is to either manually adjust for the different modes or set up one sub for music and then bring in the second sub for movies. As such, you could dial in the second ( less articulate sounding ) sub for movies with slightly more boost and leave the one ( better sounding ) sub on all the time for music.
Personally, i would prefer and recommend using identical subs as i think this works better. I have "mixed and matched" before though, so it can be done so long as you have patience and are willing to tinker with various settings. Sean