I do not put puppy pads in our crates. But then I use the only-big-enough-to-turn-around crate sizing. IMO, a puppy pad in the crate would encourage pooping and peeing in the crate and with the small size, I don't want that. I use a little blanky or towel that's easy to wash. Actually not having anything is messier than a blanket (or pad). If they pee and there's nowhere for it to go, it gets all over the crate and the pup. With a blanket/towel, it soaks up and isn't as messy.
When Coby first came home he pooped and peed in the crate every day and night no matter how diligent we were. But finally one day within the first couple of weeks, that was over and no problems since.
So patience.....