Preheat oven at 350 degrees. Slice squash and chop onion. Boil these together in a pan of water until squash is tender. Drain; add butter, salt and pepper. Set aside.
In another bowl, mix sour cream, soup, and 1/2 stuffing together. Add squash mix and pour into a non-stick 13x9 baking dish. Cover with cheese. Mix remaining stuffing with 1 cube of butter (melted). Spread this on top of the cheese and bake for 30 minutes.