Let's see if I can help with this any...

If the speakers are set to large, then the crossover point is disregarded - the speaker is considered to be full range, and no bass management is applied. If the speakers are set to small, then the 950 tries to help the speaker out by applying the selected crossover so the sub can cover the lower octaves. If the mains are set to small, any signals sent to those two speakers (be it stereo or surround) will go through the crossover and have low frequency data sent to the sub. If the mains are set to large, then nothing from those channels will ever go to the subwoofer.

I run Studio/60's and an LFM-1. With that combination, I've used small with a 60Hz crossover. The Studio/100's go about 2Hz lower than the 60's - they are physically large, but their -3dB point is -28Hz (-2dB point is 44Hz). I'd suggest trying small and the 40Hz crossover initially. With some music, the sub will not be very active at all, but that's not the fault of the setup. Most instruments do not go below about 50Hz even on the lowest notes, so most CD's have very little material there to be crossed over.