I used to have an outdoor/indoor cat for almost 7 years, until some kids were seen grabbing her and driving off. Once you let a cat out on its own, it can very easily become and outdoor lover and not want to come back in, just like mine, especially if it thinks you won't let it out again. Kittens are too small to let out, too many dangers for them. And you can't be there contantly to let them out when they need to go to the bathroom, just like small children, they cannot hold it for very long, and if you're not home even for a short time and those kittens need to go, they will, on the carpet, in a plant pot, whereever they can. I had a stink problem too with my cat. I have 2 bathrooms in my apt, and neither of them have a window, so there is no ventillation. My cat also doesn't always cover his poop, (a territorial thing the vet said) So I changed my litter to a multi cat litter, a covered litter box, and I scoop 2 times per day, usually right after he pooped, his pee doesn't cause any odor. Another option would be to change the food, but only if it is really bad. You don't want to mess too much with their diet since it can cause more digestive problems, but I am sure your vet can also advise on what food to use.