The bass management settings sound like a good starting point. I'd start out by setting the volume dial on the LFM-1 to around 5 (mid-point). Manual calibration is pretty straightforward: switch to an unused input and set the 990's volume to 0dB, then go to the channel calibration menu. Set the test tones to "manual" and scroll through each channel individually. Sit in the sweet spot and hold the SPL meter with the mic pointed at the ceiling (set to C-weighted, slow, and 70dB scale). Adjust each channel to achieve 5dB on the meter (which equates to 75dB, or reference level). You'll probably end up tweaking the sub a bit even after this. SVS has a lengthy list of bass demo material that might help you find some good low frequency samples.