Cook squash and onion in a small amount of boiling water 10 to 12 minutes or until vegetables are tender. Drain; set aside.
Preheat oven to 350°.
Melt margarine in a medium, heavy saucepan over medium heat. Add flour; cook, stirring constantly, 1 minute. Gradually add milk; cook, stirring constantly, until mixture is thickened and bubbly. Remove from heat; add cheese, salt, and pepper, stirring until cheese melts. Add squash mixture; stir well.
Spoon squash mixture into a shallow 1 1/2-quart baking dish coated with cooking spray. Sprinkle squash mixture evenly with breadcrumbs. Bake at 350° for 20 to 25 minutes or until mixture is thoroughly heated.