NEVER do any sort of punishment if you did not catch the puppy in the act. Just clean it up without a fuss (preferably when the pup is not around, as they tend to want to 'help' lol). This is what I did with Nebo.....if I caught him in the act, I would firmly say "Outside!" and I would hurry and put him outside to finish. There's really no need to pop them on the bottom, or anything like that. You don't really need to "punish" the puppy for peeing in the house....if you punish them too much they think "peeing is bad" and will go when you are not looking. My sister would yell and throw a fit at her pup when he did his duties in the house, so he started doing it in corners and places where she couldn't find it. You just need to teach them that potty is not bad, there's just a better place for it...outside. And no, don't use the crate as a punishment. The crate should be like the puppy's den, she should enjoy being in there (well, eventually of course...crate training takes time)