I have dual Submersives, an SMS-1 and an Onkyp Pro 885 with Audyssey MultEQ XT. Here's how I set things up:
First, I set the SMS-1 to Preset 6, which bypasses the EQ. I set the SMS-1 Volume at 15. Then I set any other setting on Page 2 the way I want them. (I generally shut off the crossover, set the LPF to 5 Hz and 6 dB, Phase to "0", etc.)
Next, I set the subwoofer trim to "0" in the Onkyo Pre/Pro. Then, I turn on the Subwoofer Level Calibration tone, and, using an SPL meter at the primary LP, I set the subwooferss volume control(s) so the SPL meter reads 75.
Next, I run Audyssey 8-position Room Correction. This sets the levels, distances, speaker types and crossovers. I try to adhere closely to the Forum Setup Guide:
When I'm finished, I check the subwoofer trim levels Audyssey set. It's always "0" +/- 3. I also check the crossovers, and I usually need to reset them. I usually raise them, (never lower), where needed.
Then I check the distance Audyssey sets for the subwoofer. It *should* be about 4 ft. longer than the actual measured distance. (This accounts for the "latency" in the SMS-1. It takes a few milliseconds for the SMS-1 to process the signal. Setting the "distance" by ~ 4 ft. longer, delays the *speakers* by that same amount of time, getting them back into time alignment with the subs.
Next, I go to the SMS-1's and change from Preset 6 to Setup. I then use the manual EQ to smooth out any final FR abnormalities at the primary LP. I also check the EQ curve at the other LP's to ensure I haven't made anything worse.
Last, I use the SMS-1 volume control to ensure the device has "unity gain". (The cuts and gains invoked by the EQ bands can change the overall volume level. Using the SMS-1's volume control gets the overall gain back to it's original level, or "unity gain"). To do this, I put the SPL meter back at the primary LP and play the subwoofer calibration tone from the Onkyo. I reset the level of the sub(s) to 75 dB. At the same time, I re-check the levels of all the speakers to ensure they are all at 75 dB.
So, that's how I do it. It may work for you also. Good luck.