Our 7 puppies were trained, at 3 weeks, to pee and poo in a cat litter box (introduced into their whelping pool.) In week 4, we moved them to a kennel with a small, fenced yard.
Outside the kennel, we added a litter mat and a larger litter box. The mat cleaned litter from puppy feet, but a few puppies would stop to pee on the mat. To solve that, we put the small litter box in the back of the kennel. Indoor bathroom plus outdoor bathroom. Things were good for a week.
Now, at 5 weeks, we opened up a big play space, with the litter boxes farther away. The litter mat catches litter at the entrance(exit) to the boxes.
All the puppies are able to walk in and out, but the big ones pee on the litter mat even more. It's no longer working to contain the litter. Pee and litter makes mud, and puppies track mud everywhere.
How do we solve the problem of puppies peeing on the litter mat? It's never poo--they all go in the box for that. We spray after they pee on the mat, but they are not deterred.
P.S. These are foster dogs from a shelter. Momma and 7 puppies will be spayed/neutered before they are adopted.