I marked my Light Brahma x EE with greenfood coloring with a q-tip as they hatched, the eggs were marked as collected, so I could tell them from my Pure Light Brahma chicks.
food coloring will stain the down so it will be there so long as the down you stained is there... the head and belly last the longest. Then when that down grows out you can use multi colored zip ties, I got 2 dozon from the dollar store or you can get them in multi colors at Home Depot or Lowes... I don't know what their prices are but I know they have them.