Set up a litterbox in one corner of the pen. Keep their sleeping/eating area on the other side of the pen. Before long they will start using the litterbox almost exclusively. Keep their sleeping/eating area spotless so that they are drawn to the litterbox by the scent of having peed/pooped in it before. For litter we use pine pellets made for horse stalls that we get at the farm store. You can also use pine or cedar chips/shavings but I like the pellets best.
At this age their dam is going to start weaning them, so you need to start offering them solid food. And yes, they need to have access to clean water at all times.
Here's a photo of our puppy set up with the separate areas.