In my experience, if you raise the humidity level to aid the first hatch, you will damage the later hatching chicks. When your first set eggs begin to hatch, the humidity in the bator will go up some anyway. It is less damaging to keep it no higher than 60% through all your hatches.
I would not reccomend putting them in a carton, as it is easier for the little chicks to come out if the egg is laying on its side, pointy end slightly down. You can use a very shallow card board box (with sides cut down to less thn 1/2 inch) and place all the same hatch dates in its own little box. make sure teh sides dont stick up more than 1/2 inch so that you dont retard air flow.
Hope this helps
Tony