I don't see why not. One on each shelf.
I'd arrange the shelves so the distance from the top of the oven to the top shelf and the distance from the top shelf to the second shelf are the same. Heat will bounce off the bottom of the top stone and cook your toppings on the lower pizza. You want the same thing to happen to the top pizza with heat bouncing off the top of the oven. That way, both pizzas will be done at abut the same time, assuming you put them in at the same time.
"If you want to make an apple pie from scratch, you must first create the universe." -Carl Sagan