Somebody on this board suggested that I mark mine with a little bit of nail polish on their backs. I tried it. The marking lasts, and doesn't seem to bother them. My 4 week olds look like they need their pink spots freshened up.
I have a couple of my chicks marked with little white zip ties on their legs. They are pretty hefty chicks tho. Over 2 weeks old and heavy. I left a little room for them to grow and didn't pull the tie up tight!!
I have also marked one that was showing weird symptoms with a black magic marker on it's head. I don't think I would use a red marker tho!! It could look too much like blood!
I was just careful to only get the marker on the chick's down on it's head. I didn't rub it down onto it's skin. The other chicks didn't even notice it because I think it was above their line of vision being on top of the head.