I ordered two. You've just got to manually apply the code for each.
EDIT: For clarity. After you add the first pizza to your cart the coupon will get removed. Just add the coupon code again and add the second pizza to the cart. Now both pizzas in the cart will have the discount applied. Also, you can change the size of the pizza you want by clicking "customize" or something (i faintly recall that the size options were somewhat hidden when the code was applied, but the code worked fine on the two extra large pizzas I ordered).