The trick I use is to assign the same digital input, optical 1, to two different inputs. I have it assigned to both CD and DVD. I have CD set to 2 channel stereo, and the DVD to 5 channel surround, with the center rear turned on even though I don't have one (to get around the Atlantis, JPIII and Pearl Harbor problem).

I'm not sure though whether you can set the speakers to small/large based on input.

You could probably also program your remote with a macro to do the switch, but it would be tricky, and depend on the current state of the settings to work properly.