In a Dutch oven or stock pot, bring 4 quarts water and 1 tablespoon salt to boil. Add squash and cook until fork tender, about 5 to 7 minutes. Remove and transfer to blender.
Return water to boil. Add macaroni and cook until al dente, about 10 minutes.
Meanwhile, heat butter in a large skillet over medium low heat. Add onions and cook until softened and golden brown, about 20 minutes. Transfer to blender.
To the blender, add milk, and 1/2 cup water, and puree until completely smooth and creamy. This should yield about 4 cups sauce.
Return sauce to Dutch oven set over low heat. Stir in cheese until melted and season to taste with salt and pepper (I like 1 teaspoon salt and 1/2 teaspoon pepper). Fold in noodles and thin with more milk or water as necessary.