The bass setting on the head unit is a 1 band equalizer, same thing as a bass boost knob. Unless it is your subwoofer level output, that is different because it would control the level of the outputs from the sub RCAs, at all frequencies coming out.
If your gains are set with everything flat (like they should be), then adding a bass boost increases the input signal at a certain range of frequencies. So the amp will be trying to make more power than it can in that range of frequencies at higher volumes (because it should be set to make pretty much max rms power if you set the gains right) and the signal will "clip." This causes distortion, extra heat, and wears down the sub and the amp.
It may sound like a whole number sub because you are causing the amp to clip (where it is actually very efficient when clipping) making it louder at certain frequencies (especially if the bass boost freq is around the bass notes of the song) and can make it louder on certain songs.