If you're replacing the pinion yoke or flange, it won't really matter which way you put the driveshaft u-joint on it. Phasing is taken care of by the position of the yokes on the driveshaft itself and those don't change unless there's a slip joint involved. That yoke would need to go back on the splined shaft the way it was originally installed. Many times there's a single wide spline, making it dummy-proof.
