I think you've got a good plan, Jeff - run all three subs from the trio of sub outputs on the SMS-1 and treat them as a single entity. You can start with the Auto-EQ, but I'd definitely recommend following up with a manual adjustment. We can walk you through it if the manual doesn't get you on track, but basically the manual allows you to have much more control (each EQ channel can be moved to a different frequency and its "Q" adjusted to control how widely its effects are felt, whereas the automatic mode leaves those settings at their defaults).

One other thing to consider is playing with the crossover - if you mute the SMS-1 (which effectively mutes your subs), you can vary the crossover on the mains and watch how they respond. Then you can un-mute the SMS-1 and see how the subs and mains interact. In my case, I had a dip near 60Hz that I resolved by raising the crossover so the sub was responsible for that frequency and then letting the SMS-1 flatten out the dip. It's worth keeping an eye out for.