Neglecting the SMS-1 and instead thinking about a great sub with its own purpose-built internal EQ capability, my inclination would be to let the sub's EQ do the heavy lifting first, and then let the processor's EQ go to work on the overall system - including the now-EQ'd sub.

To some extent that's what sort of what I've done in my main HT.

I leave the initial bass management (of all but the LFE channel) up to an Outlaw ICBM-1 with the bass management low frequencies getting directed to an SMS-1 feeding three of my powered subs which are treated and EQ'd as if they were a single unit by the SMS-1. The LFE channel feeds an even more potent single sub with lots of tweakability. I've used the SMS-1's display capability to use that sub's onboard EQ capability to smooth out its response. And then Audyssey sits on top of the whole shebang.

Other than the fact that I don't like what Audyssey then does in the non-bass frequency range (and hence I don't use it) I think combining these capabilities in this way makes most sense in my set-up. It's certainly much better (in the bass regions) than Audyssey alone - perhaps due to my multiple sub set up.

Maybe Trinnov will be better.