To answer your question a little more clearly:
1st - Center your wheels in the wheel wells using the lower control arms as best as possible. Measure from front of rim to a good known location on the frame that is the same side to side, we use the frame weld which is usually about 15" in front of the tires. Make this measurement the same, this will make sure the rear is pointing STRAIGHT.
2nd - Adjust the rear side to side to center it in the body using the upper control arms. If the rear needs to go to the drivers side either lengthen the passenger upper or shorten the drivers upper.
3rd - Adjust BOTH uppers EQUALLY to set pinion angle.
Apply and repeat!
Hope this helps, if you have any questions on this feel free to ask.
Mike