There are other methods but this is one that works for me.
After removing the carrier assembly from the rear end:
1. Using a center punch make a mark on the carrier somewhere that WILL NEVER MOVE OR EVER CHANGE e.g. the bottom half of the cradle for the side bearing adjusters. - refer to the blue star in the illustration
2. Then make another mark with the center punch on the diff itself - refer to the orange star in the illustration

photo courtesy of Weir Performance
3. Take some venier calipers and measure the distance between the marks when parallel and that's where the diff needs to be for it to be centered on the pinion gear.
Remember, this is only for when you're just removing the differential from the carrier for what ever reason e.g. replacing side bearings, installing a mini spool, boredom...etc...etc...The pinion gear is NOT removed or adjusted at all.
If you were to remove the pinion gear it's highly advised to replace the crush sleeve (get the weir "crush" sleeve! It's weir-th it) and apply the necessary shims to correct it's teeth depth mating with the ring gear. You may be able to perform a similar measuring trick to the original pinion before its removal i.e. a flat ruler across the carrier (with the diff already out of course) and with an accurate metal architects ruler measure from the top of the pinion gear to the ruler or sturdy flat edge you laid across the open carrier space.
Again, this may not work if you're replacing the pinion and/or the ring gear as the machining between manufacturers will differ. You'll then need to employ the appropriate methods in setting proper backlash and pre-load.
Have fun y'all!