Cut the top off each bell pepper and remove the stems and seeds. Fit the peppers down into a large oval slow cooker. Place a medium pot of salted water over high heat and bring to a boil for the pasta. Cook the pasta according to package instructions.
Meanwhile brown the sausage in a skillet and break apart with a wooden spoon. Once browned add in the chopped onion and sauté another 2-3 minutes. Add the cooked and drained pasta to the skillet, followed by the pizza sauce. Stir in 1 cup shredded cheese, then spoon the mixture into the empty peppers.
Cover the slow cooker and turn on low for 5-6 hours, or high for 2 1/2 - 3 hours. Once the peppers are soft, sprinkle the remaining cheese over the tops and arrange the mini pepperonis over the piles of cheese. Cover again, and slow cook another 15-20 minutes. Serve warm!