Preheat oven to 350 degrees. Place squash in a large saucepan with onion. Add enough water to cover; bring to a simmer. Cover, and cook until squash is tender, 10 to 15 minutes. Drain, and mash slightly in a colander, pressing to remove as much liquid as possible; transfer to a large bowl.
Add 1/2 cup cracker crumbs and 1 tablespoon butter to squash. Season with coarse salt and ground pepper; mix well. Transfer to a shallow 8-inch square baking dish. Sprinkle with remaining crumbs; dot with remaining tablespoon butter. Bake until golden, 25 to 30 minutes.