Whilst they are little I would recommend a very shallow baking tray for the cat litter. They will find it very hard to climb into anything with higher sides. The mother cat will soon teach them to use the cat litter.
How old are they now. If they are still very young they would be better housed in a smallish area, together with their cat litter and water, where they still have enough room to run around a little and mother cat can get in and out easily herself. A very large cardboard box, perhaps? You can obviously then get them out and supervise them when you want to and supervise them more.
You need to get this sorted out quickly. Tiny kittens will learn to use cat litter very, very quickly so get them into the habit now, otherwise you will not get rid of the problem.
As for the existing smell, I agree totally with Jules77 about Simple Solution.