No you leave them in the incubator on till they have fully come out of there eggs shells. I would also leave them in there for another 1-2 days but thats just me and then put them into there new tubs with damp paper towl. untill there 1st shead then they should be moved on to dry paper towl or what ever eles you use as substrate.
But how will they breathe in the bator? Cuz I have mine in a tub with no holes. Also is there a reason you have to leave them in the bator? Whats the difference between leaving them in the bator and putting them in an enclosure?