The goal is to have the included angle of the yoke to driveshaft be the same at the transfer case end as it is on the axle end. Actually, at static ride height while the Jeep is sitting still, the pinion on the axle should be a few degrees towards the pavement so that when you load the axle under power, the two angles match (axle and t-case ends).
So what you need to do is get some measurements off each end, figure out how far off the two are, and then shim the axle to the correct position. SOME TIMES, you need to shim the axle with a caster wedge AND drop the transfer case down, but not always.
OHHHH...i forgot. This is for a standard shaft.
FOR CV SHAFT:
The rear axle pinion should be directly in line with the driveshaft when under power. Meaning there should be 0 degrees of included angle at the axle end so that the CV is doing 99% of the angle change work, and the axle end is handling the rest as the axle comes on and off power.