Periodically I like to mark my ammo for whatever reason (different powder, different primer etc.). I used to use a sharpie or other pen type marker, I found a couple old bingo daubers that I stole from the wife. These work great as they will mark the entire head of the casing, they come in many colors, you can get them for a dollar or less at the local "Dollar Store" and the ink comes off during cleaning or tumbling. I have drilled out a wood block that I use to stage bullets, I can line them up and daub until I cannot daub anymore, if you use some sense, it doesn't make a mess.
Just thought I would share in case you hadn't thought of it before. Here is a link in case you are not sure what I am talking about: us-bingo.com/bingo-daubers.html