How to deal with newborn kitten bodily waste?

As I understand it, the queen (cat-mum) will help the kittens to defecate and care for the enclosure to stay clean.

Toileting

Kittens are unable to pass urine or faeces without assistance for the first few weeks of their lives so the ano-genital region – the area around the bottom and the urinary opening of the kitten being hand-reared – needs to be stimulated using a slightly damp piece of cotton wool before and after each feed to encourage toileting. The mother would normally do this by licking the rear end of kittens before, during and after feeding.

(source: hand out from www.cats.org.uk )

I assume, that the queen will lick off the faeces of the kittens, because it is not much, maybe some drops, in the first weeks. It is logical, that there is some mechanism, because cats lived decades without human care, and their nests were not getting foul :)

Later, when the kittens could move themself around, the queen will teach them the places, where it is allowed to defecate. The nest will not be such a place :)