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Blue Kote every 3-5 days on the tops of their heads. Since you are only sorting into two groups, it won't be as tough as marking each chick with a number or pattern.
Or you could put a hole in the chick's webbing for those 3 chicks. You can do it the same way they pierce ears if you have a helper. A small diameter nail with large head, a small scrap of wood, hold the chick's foot stretched out to reveal the webbing and hit the nail BARELY through the webbing then pull the nail out of the scrap wood. It sounds horrible but it is the exact same as the toe puncher.
If you like toe punching then they sell toe punches that look like finger nail clippers.