On a Detroit-style pizza, the pepperoni is normally placed under the cheese and sauce. The original idea behind this dates back to the 1940s when the original Detroit pizza creators felt that the pepperoni juices would soak into the dough to give it a unique flavor.
Additionally, we find that the pepperoni helps create a barrier between the dough, the cheese, and other toppings. Cheese and most toppings have a high quantity of water in them that is released during cooking. This water causes the top layer of dough in most pizzas to remain very soft and almost raw. While no amount of layering will prevent this, we do feel the pepperoni helps to minimize it.