Yes, the processor normally can control the gain on the sub when you calibrate it using a multi-channel pre-pro.
2 responses Add your response
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.