Preheat the oven to 350 F. Cook pasta according to package directions. Drain and place into a large bowl. In a large saucepan over medium heat, melt butter, add in flour and cook for a minute to brown.
Add in the milk, salt, pepper, colby jack cheese, and cheddar cheese. Cook the mixture until the cheese has completely melted and the sauce has thickened.
Mix the sauce with the pasta. Spread the mixture into a greased baking dish. Top with the remaining cheddar cheese and fried onions. Bake for 20-25 minutes.
