My experience with integrating the SMS-1 in with the 990 suggested that keeping the 990 "in the way" for bass management was better, for several reasons. One was the nature of the high-pass output, which as you've discovered is a fixed 80Hz signal. The other is that by only feeding the subwoofer signal to the SMS-1, I am keeping the signal path for my front channels as simple as possible. As a result, I disabled the SMS-1's bass management - I use it solely to deal with equalization. I did bump the crossover on my fronts up from 60Hz to 80Hz so that the SMS-1 could help with a room effect just above 60Hz. With all four crossovers (fronts, center, side surrounds, and rear surrounds) at or above 80Hz, the only speaker operating near that problem spot is the sub, and the SMS-1 is correcting it, so "problem solved."

If you set your fronts to small, I'd recommend at least a 60Hz crossover. Even if you do cross them over lower than that, you should adjust the crossover to at least 80Hz when setting up the SMS-1 so that the SMS-1's test tones actually get to the sub.