I've been looking at doing a system in my car also. As far as getting controll of the crossovers, For me the best option is to integrate a rockford 360.3 signal processor. It will connect to your factory radio, and make the signal coming out of the processor balanced. Then just run new amp/amps for your speakers and sub. The JL ZR800 is a direct drop in from what I have read, all you have to do is cut the back of the dorr sub box out to allow it to breath and let it run as an IB setup.
Also the processor is 31 parametric band eq with L/R adjustment, phase, and time alignment.
Also the processor is 31 parametric band eq with L/R adjustment, phase, and time alignment.