Preheat the oven to 350 F. Cook pasta according to package directions, drain. Melt butter in a large saucepan over medium heat. Add in flour, and cook for a minute to brown.
Add in milk, colby jack cheese, salt, and pepper. Cook over medium heat, while whisking constantly until the cheese has fully melted and the sauce has thickened.
Mix sauce with pasta and 1/2 of the fried onions. Spread pasta into a large greased baking dish. Top with cheddar cheese, and the remaining fried onions. Bake for 20-25 minutes.
