I agree with GotGarlic's suggestion of pre-cooking the pepperoni a bit to get rid of the excess grease.
By 'pizza cheese', do you mean mozzarella? You could layer the lightly cooked and drained pepperoni on top, sprinkle with the mozzarella, and put it under the broiler for a minute or two (watch it carefully) at the end of the baking time.
Another alternative would be to add crumbled cooked (and drained) bulk sausage to the mix and bake according to directions. Add some cheese and bread or cracker crumbs on top 15 or 20 minutes before it's done baking.