If you can disable the crossover on your sub, I'd recommend doing so - the 990's bass management makes it unnecessary. If you can't disable it, AvFan has exactly the right idea: set the sub's crossover as high as possible to keep it from interacting with the 990's crossovers.

I'd start with a crossing the mains over at 80Hz or 100Hz, the back speakers at 60Hz, and the center at 80Hz. Once you do that, play with a few movie passages that you're familiar with - you may want to tinker with the crossovers for the mains and center a bit to find a comfortable balance. The goal is for the transition from speaker to sub to be as seamless as possible.