*waving at YaYasMom*
Have the babies finished with their meds yet? You know, a prolonged course of antibiotics can cause a little stomach imbalance and soft stools.
I agree with confining them, even though they are sad about it - bless their hearts, they have had a time of it, haven't they? I usually do the same thing with my babies until they get the hang of it. And when they are ready to explore the house at large, I place small litter pans in every room, just in case. Little ones can't seem to hold it as long and they do have accidents if they don't see a pan nearby when they realize they gotta go now! Too busy playing and being kittens for such potty business! *grin*
As for the stains, I hear ya ... *sigh* ... get you a nice big bucket of hot water and pour some Oxy-Clean in with it. Get a nice large rag and saturate the area first, allowing it to sit a minute before wiping it up. If you have a carpet shampoo'er, you can put Oxy-Clean in with your water. Just don't use your regular shampoo. You don't need anything but the Oxy-Clean and hot water.
Allow the areas you cleaned to air-dry and then use the Nature's Miracle or other enyzamatic-type cleaner. You can also put the Nature's Miracle in with your water in the carpet shampoo'er.
This should pretty much eliminate the odor and the stains, and if you put a little litter pan in every room the kittens have access to, you might find the accidents happening a little less frequently.
Remember to breathe ... or not until after you cleaned good. *wink*