donovanhebard, did you get your issues worked out?
When setting up the audio system in a car, you should EQ each side of the car separately (provided your EQ has separate adjustments for right and left and you are trying to get the car to sound good from both the driver and passenger side). After the initial setup of each channel, check both together (stereo). Do not boost any frequencies when adjusting both channels together, only cut frequencies. Try using both correlated and uncorrelated pink noise when EQing each channel separately and together. Set the EQ at an average between the 2. Do a lot of listening to well recorded audio tracks between EQing (like something from Sheffield Labs). And don't try to go for a flat (straight line) curve. Just get rid of peeks and dips. To do this properly, it will take a lot of time over the course of a week or two, depending on how flexible your processors are.
Before you do any of this you should set your gains from each piece so that the signal does not clip, then when you get to the amp(s), set the max amp gain to a 3:1. In other words, set the amp gain to just below clipping, read the voltage, then multiply that by three and set the amp gain to that, then cut the gains from amp to amp to balance the sound. Also, the xover points and slopes should be set before EQing to get the car sounding as good as possible. The EQ is only used to smooth thing out.
Also, make sure that, if you have time delays, they are turned off before EQing the car (they should be the last thing set). You will probably end up with a small dip at 250hz-400hz that can not be entirely corrected (if you are running speakers in the doors).
*Kick panels would be better to eliminate cancellation, would widen the sound stage, and decrease the path length differences of the right and left channel.
Another trick that may help, before eqing. If your sound stage is low, try reversing the polarity of one channels tweeter and the other channels mid. I know it sound wrong, but it usually bumps the image up about a foot. And with the amount of reflection points in the car audio environment, it will most likely focus the image better and you should not notice any loss in the mid-mid bass range that one would expect from doing this. Also, it should help the center image from both the right and left seating positions.