Heat oven to 375°F. Spray 2-quart round baking dish with cooking spray. Cook and drain pasta as directed on box.
Meanwhile, in 12-inch skillet, melt butter over medium heat. Add onion; cook and stir over medium-high heat about 5 minutes or until soft and beginning to brown. Stir in thawed squash, chicken broth, thyme and salt. Cook and stir 3 to 5 minutes or until slightly thickened. Stir in 1/2 cup of the cheese.
In large bowl, toss pasta with squash mixture. Spoon into baking dish; sprinkle with remaining 1/2 cup Parmesan cheese.
Bake uncovered 10 to 15 minutes or until hot and cheese begins to brown.