It may seem counter intuitive, but don't point the projector towards the screen. Literally, point the projector straight ahead. Use a level, and level the side and front, and make sure the front face of the projector is square with the wall that the screen is on. Only then, use the lens shift to put the image on the screen, because it will probably be off at that point. Geometry errors should be minimal at this point. Fine tune the squareness of the picture by slight tilting or rotating the projector and readjusting the lens shift.
If the screen is perfectly level, and the projector is perfectly level (from left to right, i.e. 'roll' I believe), you shouldn't have to touch that particular position at all.