Well, another thought is this: use the SMS-1 to EQ the low frequency all the time, then run the Audyssey to EQ the upper frequencies (knowing that the low frequency is already EQ'd flat).

As for the crossover, it looks like I really hadn't mulled it over enough yet. I do see a good reason for you to use the SMS-1's bass management now - are you going to set the mains to "large" in the Denon so that the mains only have bass management applied at the SMS-1?