Yes that's where you put the shim for pinion depth. The smaller shims by the outer bearing are just to set the preload on the bearings. I wouldn't worry about them even being there right now. Just leave them out and keep bumping the nut just to get your desired drag. On a Dana 60 it should be 20-30 in/lbs of drag turning.
The reason I say just to leave the preload shims out for now is because you are not final assembling it at this point. You are probably going to have the pinion out a few more times just setting your depth. Once you get it figured out then you can figure out your preload shims.