In a saucepan, cook squash in enough water to cover until tender. Drain. in a skillet, melt butter over medium-high heat. Saute onion until tender. Place squash in a greased 2-qt. casserole. Top with the onion and half the cheese. Beat the eggs, milk and seasonings together. Pour over the squash. Top with remaining cheese; sprinkle with bread crumbs and nutmeg. Bake at 325° for 30 minutes or until set and lightly browned. Serve immediately.