Preheat oven to 350°F and spray a 10x15-inch rimmed baking sheet with nonstick spray.
In a large pot or Dutch oven, bring squash, water, onion, and 1 teaspoon of salt to a boil over medium-high heat. Reduce heat and simmer until tender, about 7 minutes. Drain and set aside.
Line bottom of prepared baking sheet with butter crackers. Top evenly with 3 1/2 cups of Cheddar cheese and bake until melted, about 5 minutes. Remove from oven.
In a bowl, whisk together sour cream, mayonnaise, heavy cream, garlic powder, pepper, eggs, and remaining 3/4 teaspoon salt.
Spread squash mixture over melted cheese, then pour egg mixture evenly over squash.
Top with remaining 1 cup cheese. Mix crushed crackers with melted butter and sprinkle over the top.
Bake until center is set, about 25 minutes. Let cool for 20 minutes before serving.
Notes
This casserole holds well for a potluck and reheats beautifully. The buttery cracker crust adds a nice crunch to the cheesy squash filling.