Ideally, the amp's gains should be set before the auto tune. The auto tune is supposed to set the levels between speakers. Now, by set, I mean a rough adjustment, it doesn't have to be perfect, but if they are too low, I don't think it can raise them.
Defeat all of the tuning except the crossover, and set the gains by ear so that the high end sounds balanced with the door speakers, and the music is as loud as you'd expect considering the volume level on the headunit (max undistorted output before the max volume on the headunit), then rerun the tune, but don't change the gains afterward, unless it's a very small change.
Personally, I prefer the vocals and highs are both at dash level, and the midbass in the doors, as it sounds like everything is higher up near ear level, rather than a lot of the music down in the doors, but you tried that and had issues, so do what works for you.
I don't want to sound insulting, but are you sure the speakers are connected to the right channels? The white and grey go to the dash, and the purple and green to the door speakers.
You can also somewhat trick the auto tune. If everything is set right, but you want more treble, lower the treble a little on the headunit, then rerun it, then set the headunit back to 0 for treble, or any combination of bass, mid and treble.
I'm using a pretty sophisticated DSP, and I've retuned it numerous times. I'm pretty close now.