Preheat the oven to 350 F. Cook pasta according to package directions. Drain. In a large saucepan over medium-low heat, melt butter. Add in flour, and cook for a minute to brown.
Pour in milk, salt, pepper, grated parmesan cheese, and 1 cup shredded cheddar cheese. Continue to cook the sauce, while whisking until the cheese has fully melted, and the sauce has thickened.
Mix the sauce with the cooked pasta. Spread out into a greased baking dish. Top with the remaining shredded cheddar cheese. Bake for 20-25 minutes.