if i was to dismantle my atlas diff to get the side gears out, should the crown wheel etc be marked so its fitted in the exact position on the carrier?

I'm not intending in putting it back together myself, i'll have a specialist do that, but i need those side gears out, and possibly some machining on the carrier

don't think you have to go to that extent but I'd still mark its position with a punch and a couple of dots, just to be on the safe side.