I didn't answer the whole question. I also suggest the center channel set to small.

I believe your sub has its own crossover controls. I would set those controls to their highest setting (160Hz?) and never touch them again. The 990's bass management will take care of the rest.
Edit: On second thought, since my system includes a SMS-1 and I don't have the manuals handy, I am not too sure that my comment above applies with speakers set to large and using only the 990 for bass management. Could someone confirm?