My amp has a setting for the low pass frequency control (50-200 Hz) and my head unit has a setting for the bass center frequency (40-150 Hz). Should these two settings be set to the same setting?
use the low pass setting on the amp to set the cut off point for the sub (well, specifically where it begins to roll off at the given slope) and use the center point on the head unit for the bass cut and boost I believe.. it centers the frequency for the equalizer. Check your manual though, if it is indeed for a head unit crossover, then just use one or the other. if you use both, the Q becomes cumulative.
Q is the slope, or roll off after the XO point. If the XO point is 100Hz, and the Q is 12dB/octave (I'm assuming "2" is second order on your head unit, which is 18dB) then each octave you move away from the XO point of 100Hz, the speaker will be 12dB quieter. One octave is double, or half of the frequency from which you began, so in this case, 200Hz. 12dB is a bit more than half volume, since every 10dB is considered double the audible volume (it's a logarythmic scale) where each decibel is generally considered the least perceptible audible change in volume. 3dB is double the power, 10dB is about ten times the power from the point of origin.
PS, 6dB Q factor is a very shallow roll off. 12dB is about the natural roll off curve for a speaker, and 18 to 24dB is a steep roll off. 24dB is like a wall, more or less. very steep.