There is no set in stone way to get perfect sound quality. Even in ideal studio situations where the monitors are set to be rta flat across a very broad range of frequencies, the sound can still be not ideal for everyone listening to their favorite music on a daily basis.
I would suggest learning about all the settings in your head unit and following very basic rules like low pass on the sub high pass on everything else. with special consideration to the tweeter channels since they can be destroyed very easily.
Outside of that find "your" favorite song and fiddle with fading, and eq to your taste.
I don't run a fancy setup so for me i turn my sub down all the way, find the loudest bass heavy song i would ever listen to and adjust the high pass on my front stage until I can be as loud and unclipped with as much "mid bass" I can get without any worries of physical damage to the drivers. For the sub channel I run it a little hot to have more headroom. IE: when listening to trap or pop my bass knob is at about half, but when some led zeppelin i can crank that knob up to taste.
I have been through probably 15 different system configurations across 4 different cars and have never had a speaker or piece of equipment fail on me by following these guidelines. Anyone who has ever sat in my vehicles be it trailer park basshead all the way to "audiophiles" has always complimented my results.