Preheat oven to 350°F. In large saucepan cook squash and onions in boiling water 5 to 7 minutes; drain; set aside.
In separate saucepan melt butter. Add flour; whisk constantly, 1 minute. Gradually whisk in milk; cook, stirring constantly, until mixture is thickened and bubbly. Remove from heat; add cheese, pepper and celery salt, stirring until cheese melts. Stir in squash and 1 cup cracker crumbs. Transfer squash mixture to a greased 2-quart casserole and sprinkle with remaining crumbs.
Bake, uncovered, 25 to 30 minutes or until mixture is thoroughly heated.
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