Your amp is weak, or your sub is weak. You want the bass to maintain at high volumes, you have to feed it heavy....like little shop of horror, "feed me Seymore." You will pretty much always have enough power for the high end, so it is constantly being powered as the volume goes up, but the bass needs even more power as the volume goes up, so it eventually gets left behind. That's the simplest way to put it. You really want to go up, get the sub a dedicated amp. Another good idea is to separate all the speakers frequency range if your setup allows that. That way the amp isn't working harder trying to feed all the speakers the entire frequency range and having the speakers do double duty. Sub...50-150 roughly, Mid...150-10000, high....10000+....off the top of my head, it's been a long time since I messed with this. There are other factors and psycho acoustics that are playing a part in this, but that is the simplest way to fix your issue and the easiest to get started.
As far as clipping the mic, that is to pic up cabin noise to automatically turn the system up as road noise gets louder and turn it down when needed. There should be a setting in the car to turn that off though if I remember correctly.