I had to mark my chicks, too, and they aren't all the same color!
I used fingernail polish (stayed away from red, as prev. poster said). It stayed on for a week or so. Also tried craft paint, which didn't work as well. I actually put the first dots on their heads. That worked great until very recently.. since they are losing their baby down. I have since switched to 'painting' a wing feather on each. It looks a little odd, but does make it easier to keep track of them (and to keep an eye on a specific bird if she starts to act funny).
I thought I'd have an easier time as they got older, but wow seems like they change EVERY day. For the last 2-3 days I could tell one chick apart from her twin by her 'necklace' of dark spots. Well.. noticed last night that her twin is getting them, too LOL! Personalities ARE different, but when you are talking about two chicks who are both fairly tame and friendly, but not overly so, and who both act the same in a group (probably bottom of pecking order, since neither one is pushy for treats AT ALL), then it gets downright impossible to tell. Thank goodness for colored dots!
-Meghan