Amplifiers come with Highpass and Lowpass filters to limit the extremes through the amplifier. This is not equalization. There are equalizers that you can run inline with RCA's but taking an input from a bad signal isn't going to be more difficult to equalize the way you want it to sound. Keep in mind that with signal units (a head unit or cd player) there is no such thing as a flat EQ. The stock HU is exceptionally bad. So keep in mind that the more you try and re adjust an already bad eq the more distortion and clipping your likely to add to your music.
I'm interested as to why your so resistant to replace the HU?