Okay.
Breaking it down:
When they hatch, take them out of the box. Out of the incubator. Out completely.
(IF YOU NEED TO, you CAN leave them in the box for a few days, but you don't have to)
Don't poke any holes in your incubation tubs.
Put them in your baby rack together with a damp paper towel as substrate.
Let them shed out in the baby rack together with a damp paper towel as substrate (doesn't have to be damp, you can have it dry).
Then move them unto the baby rack individual tubs.