It seemed to me like boost level on the amplifier will make it possible to by-pass the normal settings, and increase the DB level of a specific lowend frequency.
For example the amp I have will boost 40hrz up to +18db.
At the deck, it has a bass extend setting that basically boost the bass freq range, giving of a full bass sound. Its almost like it smoothes the edges. The receiver also allows adjustment for the sub output level to adjust for volume.
So depending on your listening preference the best advice from me is to set your bass to what you like. Just remember to turn your output level output down at the amplifier so you don't get a clipping problem and start burning up something.
Especially, when you get a good beat and start turning up volume you might not know while driving there is a distortion problem.
General rule of thumb, its the direct source of the power to your speaker that requires limits to be set. My prefernce is to amp all the speakers, set output level at center, turn off the LPH and LHP defaulting the amp eq settings to flat, then turn up the 40hrz boost all the way for the sub, and use the deck for EQ settings.