We do what Future Vet girl suggested. Tanner (our Lab) only gets in and out when we say he can. He goes to the door and bumps the door knob with his nose when he need to go out. (that's him asking) If he was brought in recently we tell him to go lay down. When he is out and wants to come in he always has to go the back door. We have large windows that are only about 8" from the floor so we can see what condition he is in before he is let in. If he's muddy...we go out and hose him off then bring him in and dry him off. OF course this is much easier with just 1 dog. Puppies are so silly and play and roll and jump on each other. I really don't have a good suggestion about keeping them clean. Last time I had a litter of puppies I had a porch that we could keep them on until they were dry or clean.
Be strong and courageous, and do the work. Don't be afraid or discouraged by the size of the task, for the Lord God, my God, is with you. He will not fail you or forsake you.
1 Chronicles 28:20