As you can see from the varying answers, there are quite a few different ways to do it. If you find what works for you, stick with it! Some people's incubators are forgiving enough that they can open them up to remove new chicks while other ones are still pipping and hatching. Some people have tried it and found that it tends to cause their chicks to shrink-wrap.
Personally, I like to try to stick to the guidelines. Once my first chick has hatched, I'll leave it in the bator for what I consider a reasonable amount of time so as to give the others a good chance of hatching out in optimum conditions. After 36 hours I'll have a look in and see how everybody's getting on. If the bator's getting crowded and the still-to-hatch eggs are mostly unpipped, I'll sneak in and remove the boisterous fluffies. If I do that, I'll leave newly hatched ones and weaker looking ones to dry off and get their strength up free of being trampled all over by the stronger ones. I've never had a problem with chicks becoming shink-wrapped after I've opened the bator, so I'm happy doing it. Even so, after 36 hours, if I have a lot of chicks still pipping and zipping, I'll leave the bator shut for another 12 hours or so. I've never had a problem yet, but that doesn't mean it won't ever happen to me.
You can leave chicks for 72 hours without food and water, so if you do have shink-wrapping problems, leave the bator shut as long as possible...