I label mine using a Sharpie on a piece of masking tape on the top of each clutch in a deli cup, and arrange them by hatch due date. At 80-82 degree incubation temperatures, I use a due date of 54 days, and for the boys at 88-90 degrees, I use 39 days. When the eggs hatch, I write the hatch date on the tape, and use it as the label for the shoe box in the rack. That date is what I use as their ID#s.
I keep a chart listing all of my females where I keep track of each individual's clutches laid, dates, # males/females incubated, and weights. I made up an Excel chart where I plot all of this data, and turn it into a graph so I can watch trends, get average time between clutches, incubation durations, percentages for hatch success rates, and body weights.