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I am not an expert but I thought I read that if the crate is too big the dog will often go to the bathroom in it. So the right size is important where it is not too small yet not too big. I am not for sure on this though but you may want to look into that
When our dogs were pups during waking hours we took them out every 45 minutes which I think was too much but they did get trained well so who knows. We kept our eyes on them always. If we saw one start to go we would rush him outside and then if he continued outside lots of love and praise. As time passed we went longer in between taking them outside.
Good luck