Kaji started in an ex-pen, and now nothing. He sleeps in his own bed when he wants to or sleeps in mine. I prefer he sleeps with me.
The only time I use a crate is to transport a really sick foster baby from point A to point B. It really is all about personal preference. Do whatever you're most comfortable with, or whag you feel is giving you the results you desire.
Although, I will say, isn't adding a pad to the crate counter intuitive? I though the pups were suppose to identify the crate as their sleepinf domian and not soil the inside? I may be wrong though as I didn't crate train myself.