Preheat oven to 375°. Brush sides and bottom of 13- x 9-inch baking dish with Olive Oil, then evenly spread with 1/4 of the Sauce; set aside.
Brown sausage in 12-inch nonstick skillet breaking into small pieces; drain, if desired. Stir in shallot, garlic and red pepper flakes and cook, stirring occasionally, 5 minutes or until sausage is done. Remove skillet from heat and set aside to cool.
Combine cooled sausage mixture, 1 cup fontina cheese, mascarpone cheese, 1/2 cup pecorino romano cheese, oregano, thyme, 2 tablespoons of parsley, and black pepper in medium bowl.
Evenly fill manicotti shells with sausage mixture, then arrange in prepared baking dish. Evenly top with remaining Sauce. Bake uncovered 25 minutes or until heated through. Top with remaining cheeses. Bake an additional 5 minutes or until cheese is melted. Garnish, if desired, with remaining 1 tablespoon of parsley or additional oregano.