You should be able to turn off the surrounds, so I'm a little confused by that.

As for the sub behavior, you can count on the 990's crossovers to take care of things for you, but you may need to tweak your 990 settings a bit. Have you considered running mains as small and sub as "on" (or "yes", I forget what the exact term is). The L/R+Sub is a mode that I've always thought of as better suited to running with the mains large.