Preheat oven to 350 F. Cook pasta according to package directions, drain and place into a large bowl.
Melt butter in a large saucepan over medium heat. Whisk in flour and let cook for a minute to brown. Pour in milk and add in grated parmesan cheese, 1 cup shredded cheddar cheese and 1 cup shredded colby jack cheese.
Season with salt and pepper. Continue to cook over medium heat, whisking constantly until thickened and smooth. Mix sauce with pasta. Spread pasta out into a large greased baking dish.
Sprinkle with the remaining 1 cup shredded cheddar cheese and 1 cup shredded colby jack cheese. Bake for 25-30 minutes.