My chicks are mostly black and I mark them with a blob of water colour paint that comes in a tube. Like squeezing a little toothpaste on their head. This is NOT the dry stuff in tablet form. Gloppy stuff, in tubes.
Yellow, white, orange, red, green, purple, blue..how many colours do you want? Splot, on the head. It does flake and drop off as fluff grows out, but it's easy enough to re-blob when one gets too faded. And once they are a bit bigger, then move on to banding of some sort.
They look like a collection of punk rockers. BUt it is easy to see at a glance who is who.
I find this very effective for short term marking.
About separating eggs in bator..I bought some sheets of perforated plastic from craft stores. Flat, like a placemat. Cut it into 2 or 3 inch tall strips, depending on the clearance in your bator. Attached these strips as needed with pipe cleaners ( I use them instead of twist ties, can cut to length) to make longer strips, then make round corrals, size as required. If you make them too short, chicks can glump out. I like that the strips can be wired and unwired to make bigger or smaller for next hatch.