Hi Jim; you're going to want to set all your speakers to small and make sure your crossover on your sub is set as high as it goes so that it doesn't come into effect. The large setting only goes for full range speakers, which the M1s, or even M40s are not.

If I could give a big recommendation, I'd say that you should try to properly calibrate your system to bring your sub to life and your system more balanced. For $15 you should buy the new Sound and Vision calibration disk, and then pick up the analog radioshack SPL meter for $30. After you get these two items you'll be able to perfectly calibrate each individual speaker level and proberly calibrate the levels on your sub. Without proper calibration you're not going to get the best out of your system. With these two relitively cheap additions to your HT arsenal you'll probably be probably notice a huge difference in your HT experience.

Proper calibration is definitely the way to go IMHO.