sub with two sources - can processor control gain?

I am considering building two systems, one for theater and one for two channel in the same room. I'd like to use a pair of subwoofers for BOTH systems (by using both the RCA and balanced inputs), and I'd like to do it without having to fiddle with the sub settings. My plan is to get a pre-amp for the two channel rig that has bass management built in lIke the new Emotiva:

I would then tune the subs to match the two channel rig, with the crossover set in the pre-amp, leaving the sub itself to run wide open and only adjusting the gain on the sub.

Obviously the processor will do a crossover to match the l/c/r etc. My question is, cant he processor control the gain also, or will I have to turn it up manually on the sub??
Yes, the processor normally can control the gain on the sub when you calibrate it using a multi-channel pre-pro.
Yes, it can control the gain on the sub as part of the calibration but there is a definite possibility that the gain setting selected for the 2 channel rig will put the sub beyond the processor's adjustment range. That will depend on the relative sensitivities of the stereo and theater speakers and the relative sensitivities of the stereo amp and theater processor/amps.

Lots of variables.