I prefer wood shavings and using a little "potty room" connected by a threshold to your puppy box. It acts as a letterbox of sorts, and the shavings keep the smell to a minimum and there is no danger of them ingesting some of the pellet type things people are using in puppy boxes of late

hardwood pellets fuel. Available at some, but not all, Home Depots. Clean, easy to use and very inexpensive.