"1. Could you please give us a quick tutorial on how to adjust crossover points and changing phasing to adjust, imaging and stage height."
Totally dependant on the components you're using and how they are installed. Generalizing:
6db/oct: Best phase and amplitude response (Butterworth). Worst off axis performance and modulation distortion. 90 degree phase shift. Stresses drivers such as tweeters and delicate midranges, as 6db/oct isn't enough to limit excursion in many cases. Very sensitive to driver alignment, both in relation to each other and also the axis of the drivers themselves. Best results usually come with installs where the tweeter is very close to the mid, and careful attention to positioning is taken (kick panels, angled door).
12db/oct: 2nd best phase and amplitude response. Less sensitive to driver misalignment than 1st order crossovers. May still be too shallow for certain drivers. A natural crossover for a car, gives a good response. Good for installs that are slightly off axis, and drivers that are decently close to one another, more forgiving than a 1st order crossover in that respect.
18db/oct: Good amplitude and phase response. The steeper slope can minimize modulation distortion and it improves off axis performance. Less sensitive to driver misalignment. Good for off axis installs like a stock door panel, and the tweeter being further from the mid.
24db/oct: Can produce a very flat amplitude and phase response. Steep slope equals least modulation distortion. 360 degree phase shift, so the drivers are "in phase", but the time alignment is off. Least sensitive to driver misalignment. These are typically used in off axis installs and give good results if you want to locate the tweeter far from the mid.
Phase alignment or time alignment does essentially the same task. You're simply trying to align the drivers acoustically to provide a coherent output to your ears. Best done with experimentation, as even with equations the end result can and will be affected by the environment, especially talking about a car with multiple reflections to distract the originating signal.
"2. Where abouts is the best place to put the Mic for the time alignment and where should I point it?"
Wherever your head will be.
"3. What is the best way to EQ the system with the Built in 13 band EQ? " Rent an RTA and see the frequency response, and adjust as needed. If that isn't an option, go by ear, you'll need a reference system (a *good* set of headphones make an excellent reference for tonality)