Grandtech,
Are you using a video monitor to view response during the set-up tone sweeps?
If so, you can see the impact of adjusting any of those controls. As you adjust them, the change in the output of the sub will be reflected on screen. Once you see the change, you can listen for it. In my case, most changes were clearly audible, tho sometimes an adjustment that produced a visible result did not produce an audible result (that I could detect, anyway).
Fine adjustment of phase may help reduce some response anomolies prior to EQ and therefore reduce the amount of EQ you'll need to "fix" the response. Similarly, you can adjust placement of the subs while viewing response to the same end - optimal placement reduces the amount of EQ needed. That way, you'll be able to "surgically" use those 8 bands to get really smooth bass response. A mammoth PITA, but worth the effort.
The slope and level controls are essential to acheiving smoothest hand-off from main to sub. That one you will see and hear.
Marty
BTW, if the software hasn't been updated since I bought my SMS-1 (it's been +/- 3 years, so this may or may not still be true):
I would strongly advise against just using the AUTO EQ function. It does not even begin to utilize the parametric capabilities in the sub and you can do much, much better via manual adjustment w/ the video readout, per the above.
Good Luck,
Marty