Prepare pasta according to package directions. Keep warm.
Melt butter in a large saucepan or Dutch oven over medium-low heat; whisk in flour until smooth. Cook, whisking constantly, 2 minutes. Gradually whisk in milk, and cook, whisking constantly, 5 minutes or until thickened. Remove from heat. Stir in salt, peppers, 1 cup shredded cheese and cooked pasta.
Spoon pasta mixture into 4 lightly greased (8-ounce) ramekins; top with remaining 1 cup cheese.
Bake for 15 minutes or until bubbly. Let stand 10 minutes before serving.