When I have kittens, I turn my big dog crate into my kitty condo. I take the divider panel that you use for puppies and put it in vertically and this makes a shelf for their bed. On the bottom level, is their litter box (inside of another box to keep the mess contained) and their food/water. This gives them space to play on both levels and the box for the litter box is their steps to the top level.
My boy - 5 year old white Boxer - thinks that all of the kittens I bring in are his. He is extremely protective and mothers them contantly. It doesn't matter is they are newborns or 4-5 weeks old when we get them. He is so big and they are usually so small that he can't carry them by the scruff of their neck so he just carries them by their heads. And they somehow know to trust him.
When the kitty condo is up, I too will leave the door open during the day and then everyone is put back in for bed. My Sissy was one of my babies. Her brother died in my arms and she had major problems. She was the ONLY foster that my tom had every paid attention too so she stayed. And she is definetly HIS girl. But when Sissy was migrating from a foster to a permanent member, she still would run to the kitten cage when she wanted to use the litter box or get a bite. It was so funny to see her out playing and then suddenly running back to the crate.