Preheat oven to 375. Mix cheeses together and set aside.
Heat olive oil is a skillet. Add the onion, peppers and garlic and saute over medium heat for about 5 minutes. Add crushed tomatoes, basil, and crushed red pepper (if using). Simmer uncovered for 15 minutes.
Mix squash well with cooked veggies and spread half in bottom of a 9x13 pan. Top with half the cheese mixture. Then spread the rest of the squash mixture and then end with the remaining cheese.
Bake for30 minutes until cheese is bubbly and slightly golden. Let cool and set for 10-15 minutes before serving.