Preheat your oven to 350 degrees F. Spray a 2 quart baking dish with cooking spray. Set aside.
Melt butter in a large skillet over medium heat. Cook squash and onions until tender, stirring frequently (about 10 to 12 minutes).
Drain squash and onions in a colander. Press with a large spoon or the back of spatula.
Transfer drained squash and onions to a large bowl. Add salt, pepper, sour cream and cheeses. Stir to combine.
Transfer squash mixture into prepared baking dish and spread evenly. Sprinkle evenly with crushed buttery crackers.
Bake (uncovered) for 15 to 20 minutes, or until crackers are golden brown and edges of casserole are bubbly.