I set my system up manually the first time (both speaker size/crossovers and channel trim), then ran the auto-setup, and the 990 made no changes to my size or crossover settings (I don't know if it even does select crossover points). It also seemed to yield very similar results both times I ran it, and those results were pretty close to what I had come up with on my own. Was there anything weird in between the surrounds and the mic that might have messed things up?