The stuffed crust of stuffed crust pizza is usually stuffed with cheese. Extra mozzarella is made directly into the crust of the pizza so that you get the extra cheesy bite at the end. I have seen some pizza recipes that use pepperoni or other toppings that are also added to the crust. This can be a bit trickier but it is possible. I like using string cheese because it melts wonderfully and is already portions and shaped ideally to go inside the crust.