Preheat the oven to 350°F (175°C).
In a large skillet, sauté the sliced squash and chopped onion in a bit of butter until tender.
In a mixing bowl, combine the cooked squash and onion with sour cream, garlic powder, salt, pepper, and thyme.
Stir in 1 cup of shredded cheddar cheese.
In a separate bowl, mix crushed crackers with melted butter.
Spread half of the squash mixture in a greased baking dish.
Sprinkle half of the cracker mixture over the squash layer.
Layer the remaining squash mixture on top.
Finish by topping with the remaining cracker mixture and the remaining cheese.
Bake for 30 minutes or until golden and bubbly.