If your input is stereo, it will remain stereo without a sub unless you set LFE+Main mode for the subwoofer.
If your input is multichannel it'll play all channels that are there as they are without any mixing. If an x.1 / LFE channel is there, it'll play it on the sub.
Setting the speakers to small with a crossover set works for the stereo mode, not for the direct modes.
It'll remember the last sound mode set per source (but also depends on the material received). You can also use the 4
quick select buttons which you can program to store the combination of source+configurations (speaker config, audyssey, etc). Handy when you want to switch between different settings from the same source.
There's also the sound mode buttons, MOVIE/MUSIC/GAME that each remember the last sound mode they were set to. And then the separate 'PURE' button. Pressing PURE for CD playback and pressing MOVIE for ..movie playback could suffice. If you want more settings changed other than sound mode, program yourself a pair of quick select buttons.
Speaker presets are handy when your room changes or you move seating/speakers for different occasions and you need 2 sets of audyssey corrections/eq/distance settings etc. Example: with and without the projector screen deployed. I'd use the quick select or sound mode buttons.