My light boys are 3-weeks older than the ones with darker down. So it will be really easy (for quite a while) to keep them separately identified..I wonder why are you getting Dark boys and Light boys, double shot of barring should lighten a chick down, maybe he is a heterozygous male(single barring) can you separate your dark colored male chicks and track their progress..
I wonder wy Punnett didnt use a better autosexing "e" allele, eb and ER are better than e+ asfar as autosexing goes