8 3/4 pinion shim question

I have a dial indicator and base, but I've just been going off of gear marking compound right now. My main question is which way should I set the pinion (deeper or shallower) because the two bearings are different heights, so when I check depth with one it won't be the same for the other. I don't want to keep trying to press the new one on and off because I don't want to tear it up, but using an old on for measuring won't get me the same numbers.