Preheat oven to 400 degrees.
In a large skillet over medium/high heat, sweat the green pepper and onion in the olive oil, stirring frequently for 3-4 minutes.
Add the chopped pepperoni and continue to cook for an additional 3-4 minutes.
Turn the heat to medium and stir in the flour. Cook, stirring frequently for 1 minute
Slowly stir in the milk along with the basil and oregano.
Continue to stir until the liquid begins to bubble and thicken.
Stir in 1½ cups of provolone and 1 cup of the cheddar cheese. Stir to combine.
Add the cooked and drained pasta to the cheese sauce and stir well to combine.
Turn the heat off under the skillet and top the pasta evenly with the marinara sauce.
Top the pasta and sauce evenly with the remaining cheese and top with the rounds of pepperoni.
Carefully place the skillet in a preheated oven and cook until the cheese is browned and bubbly, approximately 15-20 minutes.
Allow the pasta to cool slightly before serving.