Cut squash in half lengthwise, and remove seeds. Place cut side down in shallow baking pans, and add 1 inch water. Bake, uncovered, at 400° for 30 minutes or until tender. Drain. Brush inside of hot acorn squash with melted butter; sprinkle with salt and pepper, and set aside.
Combine Brussels sprouts and onions; cook according to package directions. Drain, and set aside.
Melt 2 tablespoons butter in a heavy saucepan over low heat. Add flour; cook 1 minute, stirring constantly, until mixture is smooth. Gradually add milk; cook over medium heat, stirring constantly, until thickened and bubbly. Pour white sauce over Brussels sprouts and onions; toss gently. Spoon Brussels sprouts and onions evenly into squash halves.