Well, first of all, my main objective is two channel. I have two systems, integrated together, with separate preamps, and amplifiers. Using just the .1 channel in my pre-pro was just too limiting for me in available options. (My pre-pro is an older Fosgate model, without the features currently available for bass management as in the newest models available).
I do watch the odd movie once in a while, but on satellite, I don't have a Blu-ray player.
Quite often, when I play multi-channel music, the front channel level is set using my stereo line stage, and center and surrounds (fed by a pass-through in the line stage), are set through the pre-pro. I feel this arrangement affords me the most flexibility with my set up. Most often, I don't use a sub, as the one I've had (an old Velodyne 1250X), could move my listening seat from 15' away, but was not very musical sounding. I feel I get the best sound quality from the main speakers this way.
I am not using different sources, at least in the way you mean. The sub is hooked up only one way, from the speaker outputs of my two channel amp. The switching is done via my line stage.
I hope I have explained myself adequately. I may be all screwed up in what I'm doing, but it works for me.