For EQ tuning to work, the input has to be flat. Our stock has some strange EQ setting as default, and we need to do some "magic" each time we turn on the car to get a flat input. Otherwise, there will also be limitations for the EQ as the tuning would not be accurate.
Easiest way to test this is to plug an MP3 player that has preset EQs to the AUX in of our stock player. Notice that when a particular EQ is selected, the effect is not accurate/what you'd expect. So most of the time, I had to set the EQ to flat to hear the music clearly - thereby rubbishing any benefits of the preset EQs.