Have you thought about crate training them? Maybe making them go outside? I know everyone's different but I'm a firm believer in outside is where the poo goes....
If they are kenneled while you aren't home then for the most part pups don't like to "go" where they sleep. When you are home take them out every 30 minutes at first to get them used to the idea of going outside. This does require a little work in harnessing, etc...but in the end you will not be cleaning pee off your floors
