I'd recommend just doing it through your Head Unit. Get a good head unit, like the Alpine 9855 and you have a 5 band fully parametric EQ(not the crappy semi's that come with Pioneers) or a 13 band Graphic, and full time alignment functionality, down to 100'th of a second. And fully customizable crossovers.

If you want more detailed than that, like doing a FULL component time alignment, and driver alignment then you'd want to look into a processor. Like the Alpine PXA-H900 but that will run you a good $3,500+. Which IMHO seems pretty damn pointless unless you're building a SQ Competition car.

But I do not recommend doing your time alignment through PC software. Mainly because there is a propagation delay in your HU (If you're using one) and in your amplifiers. The HU/Proc. will be designed with this in mind.

Also, as far as EQing goes. Do it by your own ears. Working in the PA (concert, theatre, and corporate) world, I have yet to hear a system that will sound as good EQing itself as it will by being hand tuned. Main reason for this, is that it only hears what the sound is like where the microphone is placed, and has no clue what things like Nodes, Anti-Nodes, Comb Filtering, etc... are. Say you place the mic in an area that has MAJOR comb filtering. and Say that one of the damages areas is 125Hz. It will try to adjust for that by boosting it up, but will never be able to fix the problem because it is a time based problem (due mainly to reflections in the car) So you end up with a car that has TONS of 125 through 80% of the car, but you still can't hear it at the drivers seat.

And as for the auto time correction, same thing applies. In such a reflective environment your Proc will have a very hard time knowing when something is a reflection, or it's the primary Impulse Response.

Just my $0.10

Best of luck with getting your system sounding great. and keep us posted on your progress.