Well i am not sure if i understood your questions, but i hope i can help you.
You need to calculate the two angles of the sun, azimuth (horizontal) and elevation (vertical). they depend from time (day of the year, time of the day) and the coordinates (longitude, altitude) that you are.
Also you need to measure the angles of the two axes of the tracker (horizontal, vertical). the tracker must face South 180 degrees (for the North Hemisphere).
Every time you calculate new angles, you must turn tracker.
For any further questions please contact me to my email kostas@kokoras.com