In the incubator I've used a box icecream tub or similar, cut out bottom and you have plastic walls for eggs/chicks of one blood line. Marker pen in different colours or food dye works fine for a week or so, then you have to top up.
If you have time, Mark each set. Eg. Mark one set with red and another with green or blue - it's easier to tell apart a faded red and a faded blue than a faded red and a non marked.