Preheat oven to 375°F. Toss squash with oil and salt on a foil-lined tray. Bake for 20 minutes or until tender, set aside.
Cook pasta for 2 minutes less than package directions call for; drain and place in a bowl with squash. Meanwhile, melt butter over low heat. Whisk in flour; cook for 2 minutes.
Slowly whisk in milk. Bring mixture to a boil, then simmer. Cook 3 minutes, stirring occasionally. Add 1 1/2 cups cheese; stir until melted. Stir cheese sauce in pasta and squash.
Spoon into 6 greased, individual ramekins. Sprinkle on remaining cheese. Bake 10 minutes.