Top is a must so that it can get crispy. I have been making some pizzas recently, and got a good tip to decrease the amount of grease that pepperoni put out.
1) Put a couple of paper towels on the bottom of a plate, and place all your pepperoni around the plate, not overlapping.
2) Microwave for ~20 seconds, the pepperoni will have cooked some and released a good amount of grease.
3) Pat down the top of the pepperonis with another towel to clean up the remaining grease.
If you do this, you wont be left with a big grease puddle on the top of your pizza.