Preheat oven to 350 degrees F (175 degrees C). Lightly oil a 8x8-inch casserole dish with cooking spray and set aside.
Heat olive oil in a saucepan over medium-high heat. Stir in green pepper, garlic, and green onions; cook until the pepper softens, about 3 minutes. Pour in marinara sauce and simmer 5 to 7 minutes, stirring occasionally.
Mix together fontina and provolone in a bowl. Spread a thin layer of sauce over the bottom of the prepared baking dish. Arrange 1/3 of the polenta slices in the dish, top with 1/3 the fontina and provolone mixture. Spread a thin layer of sauce over cheese. Repeat layers twice. Top casserole with Parmesan cheese.
Bake in preheated oven until cheese is bubbly and golden brown, about 25 minutes.