I don't know anything about pee pad training but I know that to crate train you only want to give them enough room to lay down. If they have too much room they'll poop in a corner, but they'll learn to hold it if they don't have room to go. It takes time and you have to let a young puppy out regularly because they don't have control of their bladder as well as when they get older. And don't leave them in a kennel to walk in the poop.
When Reuger was a young puppy I had him in a crate at night and when I wasn't watching him and he kept pooping in the crate. I started reading on YorkieTalk about crate training and followed the directions. It sounded so mean to just give Reuger a small amount of room but it worked. He had very few accidents in the kennel after that. Over time I just started giving him a little more room and he's 3 1/2 years old and I can't remember the last accident that he had in the crate. He still sleeps in it at night.
http://www.perfectpaws.com/crt.html