i would suggest to seperate kits from the jill,, that way it will easier to tame them and they wont learn the same behaviour of the mother
well done to you taking them on, i must confess i would have done the same
bedding wise put wood shavings throughout the entire hutch, sleeping area and run, then in the sleeping area pop a good layer of bedding in, theres a wool/paper ferret friendly thats brilliant or you could use shredded paper or dust free hay,, put plenty of bedding in as they like to make a nest out of it
otherwise i wish you all the best with your litter and hope the j