Here's what I do for bolt action... And it helps if you buy Lapua, Peterson, or any other brand that comes in its own case... Otherwise I will buy an MTM (or similar) case for that brass
The brass always stays in it's box. If I only load part of the brass then the empties stay in the box with the loaded rounds... When I fire them I leave the spent primers in the brass. When the entire 50 or 100 get fired then I deprime them all at once and mark the number of firings on the card (Peterson includes one) in the box.
Then I prep all 50 pieces at once... Tumble, Anneal, Size, Trim, Chamfer/Deburr. Then I leave a note in the box that they are ready for priming/loading.
For gas guns/high volume... Good luck. I just do the best I can to keep track.
Mike