My suggestion would be to disable the SMS-1's low pass crossover, set all speakers to small in the 990, and adjust the HD-DVD player so as to disable its bass management (all speakers large and sub on). The Monoliths have a -5dB point (not -3dB) of 28Hz, so I'd certainly run them small. You could probably go with a 40Hz crossover, but with those two LFM-1 Plusses you might also try 60Hz just to see how it does. The Aerius rears should probably be crossed over at 60Hz, possibly even 80Hz (-3dB point of 40Hz). The Cinema has a -3dB point of 80Hz, so you might actually want to cross it over around 100Hz.

When setting up the SMS-1, the fronts really must be set to small small and you should also adjust the crossover up to at least 80Hz. If you want to bump the front crossover back down to 60Hz or 40Hz afterward, that's fine, but you need the crossover that high to be able to deliver the SMS-1's test tone through the 990 and out to the subs.