Pens have a much larger place than a crate and are open from the roof. If you want to keep your puppy in a pen, then there should be two different surfaces within it if you are using it to toilet train them. The puppy should learn to differentiate between them.
The pen is basically their playing and resting area so if the puppy is already toilet - trained, do not use the pen for it. The smaller the pen the better it is to avoid accidents.