Too Many Bass Settings to Choose From

From the time the music is read from its media to the output through the subs, my bass can go through 3 different locations to alter it and I believe it's making the bass sound not as well as it could.

First, the head unit (Pioneer AVIC-FT90BT) has a few settings:
Bass:
-Phase (Normal/Reverse)
-Level (1-6)
-Freq (30?-150? Hz)
Bass Boost:
-Amount (1-10)

Second, Clarion active crossover (i mainly have it for HPF for Mid Amp & High Amp),
LPF:
-Dial (Up to 400? Hz)
Bass Boost (Mandatory):
-Freq Dial (Up to 100Hz?)
-Boost Dial (Up to +18 db)
Line Output:
-Dial (Up to 100%)

Third, Hifonics Amp
Subsonic Filter:
-Dial (Down to 15 Hz)
Low Pass Filter:
-Dial (Up to 250 Hz)
Bass Equalizer
-Dial
Bass Boost
-Dial
Gain
-Dial (0.9 to 9v?)

Sorry for a lot of "?" I am not sure about the specific ranges, but it gives you the gist. Every piece has a different range on the same line.

I am thinking that I will keep the active crossover for the High/Mid, but will plug the SUB Preamps directly to the amp. Other than that, do you have any suggestions on how I should start out. I know how to set the gain until clipping/distortion, but I am puzzled at the Eq/Boosts. For the Eq, I've read you are suppose to match your music preference. I find it hard to narrow down when I regularly listen to County, Emo.Rock, Southern Rock, 90s Hip-Hop, Alternative, 80's, Techno/Daft Punk, etc. Then whenever I use the bass boost at any point (nd this is how it is now), my bass greatly overwhelms the mids and highs. I would like a profound bass, but also in good mix with the highs/mids instead of shrienking their sound.

Any suggestion for managing the settings and blending the music is greatly appreciated.