Slice the yellow squash about 1/4 inch thick. Make them even so they cook at the same rate. Heat up your large skillet over medium heat and melt 2 tablespoons of butter. Add the sliced squash to the pan and sprinkle 1 teaspoon of salt over it. Stir the squash around gently so all pieces get coated with butter. Let it cook for a few minutes until it starts to get tender.

Chop your onion into small pieces—not too fine, but not too chunky either. Add the chopped onion to the skillet with the squash. Keep stirring everything together and let it cook until both the squash and onion get soft and tender, about 10–12 minutes. You’ll know it’s done when you can easily pierce the squash with a fork. Remove from heat and let cool slightly.

In a large mixing bowl, crack 2 eggs and beat them lightly. Add sour cream, cheddar cheese, Swiss cheese, mayonnaise, black pepper, thyme, and the remaining 1 teaspoon of salt. Mix everything together well until it’s creamy and fully combined.

Pour the cooked squash and onion into the bowl with the cheesy mixture. Stir thoroughly until all the squash is coated and the mixture is evenly distributed.

Grease a 9x13-inch baking dish with butter or cooking spray. Pour the squash mixture into the dish and spread it out evenly with a spoon or spatula, making sure it’s level.

Crush two sleeves of buttery crackers in a bag using a rolling pin or by hand. Place in a small bowl and mix in the shredded Parmesan cheese. Melt the remaining 4 tablespoons of butter and pour it over the cracker mixture. Stir until the crumbs are coated and resemble wet breadcrumbs.

Sprinkle the buttery cracker topping evenly over the casserole, covering the entire surface. This creates the golden, crunchy top layer.

Preheat the oven to 350°F. Bake the casserole for about 20 minutes, or until the top is golden brown and the edges are bubbling. The topping should be crispy and the center hot.

Let the casserole rest for 5 minutes after removing it from the oven. This helps it set and makes serving easier. Cut into portions and serve warm alongside your favorite main dish.