Preheat oven to 325 degrees F (165 degrees C).
Fill a large pot with water and bring to a rolling boil. Add yellow squash, zucchini, and onion; bring back to a boil, and cook vegetables until tender, about 15 minutes. Drain and transfer vegetables to a large bowl.
Mix Cheddar cheese, baking mix, butter, eggs, sugar, and salt with the cooked vegetables using a large spoon; stir until butter has melted and baking mix has dissolved. Fold crushed crackers into the mixture until the liquid has been absorbed. Pour mixture into a 1 1/2-quart casserole dish; top with bread crumbs.
Bake in the preheated oven until topping is lightly browned and cheese is melted, 30 minutes.