You shouldn't have to mess with any settings on the back of the sub. Just plug your sub cable into the "Sub In" or "LFE" input on the back of the sub. Set your gain/volume knob to around 12 o'clock and run your room correction. Then yes, set your speakers to small and your crossover around 80-100hz depending on your liking. If you have separate crossovers then you may set your front speakers to around 50-60hz. But the sub should be 80-100hz.
Someone correct me if I'm wrong...
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Pioneer Elite VSX-90 7.2 * DT Studio Monitor 45 front L/R * DT ProCenter 2000 * DT ProMonitor 800 surrounds * dual Hsu VTF-3 MK5 subs * VTI RF Series 29" speaker stands * DT ProMount90 wall mounts * OSD Audio WSK-100 wireless sub kit *