I don't think the auto setup adjusts the crossover settings - either way, I would do it manually. Cvinfig is quite right that the sub's crossover should be disabled if possible and adjusted to its highest setting if not. What the sub is doing is discarding all data above that crossover point - setting it to a value lower than your highest speaker crossover setting will basically throw away audio information, and setting it too close to any of the 990's settings will create two overlapping crossover slopes in series - not a desirable condition. Cvinfig's guidelines on how to select crossovers are in line with my own.