The SMS-1 has two distinct "auto EQ" modes. The first is Self-EQ mode, which can be done simply by connecting a sub to the unit, connecting the microphone, and pressing 3-2-1 on the remote. That mode should do 25 test tones, at which point it will apply adjustments to the either EQ channels. It will not do anything with the frequencies at which the EQ's are applied, sub levels, or anything else, and it will only involve the sub (the test tones are sent directly to the SMS-1's sub output, not to the outputs that run to your receiver).

The "Auto EQ" mode is similar to this, but sends the signals through the EQ outputs to the receiver, alowing the receiver to apply its bass management and do whatever other tasks it might do. (You'll want to be set to the SMS-1's input and have any surround processing disabled, so the stereo signal just goes to the mains and the sub.) As before, you'll also need the microphone connected, at which point you can press 1-2-3-4-5 to enter the setup menu. You'll probably want to adjust your volume while you're at it, but assuming that's taken care of you will simply highlighting the "EQ Mode" setting in the System Response screen and pressing "SELECT" to change from manual to automatic. This will do closer to 50 sweeps before ending, and will still not change the positions that the EQ channels are set to.

Hopefully that helped some. If you haven't done so already, I'd suggest downloading Outlaw's SMS-1 Guide (click here for the PDF). In addition to the notes on pages 14 and 15 regarding this, there is a lot of other good information in there.