Melt 2 tablespoons of butter in a large pan over medium heat. Preheat the oven to 350 degrees F.
Add the squash and onion to the pan and cook for 5-6 minutes or until vegetables are tender. Season with salt and pepper to taste.
Remove the squash mixture from the pan and place in a large bowl. Cover to keep warm.
Wipe out the pan with a paper towel.
Melt 2 more tablespoons of butter in the pan. Add the flour and whisk to combine.
Cook the flour mixture for 1 minute, stirring constantly.
Whisk in the milk and cook for 2-3 minutes. Add the cream, thyme and salt and pepper to taste.
Cook the sauce for an additional 2 minutes or until just thickened.
Coat a 2 quart baking dish with cooking spray.
Pour the sauce into the bowl with the squash. Add 1 1/2 cups of cheese and stir to combine.
Pour the squash and cheese mixture into the prepared dish.
Sprinkle the remaining cup of shredded cheese over the top of the casserole.
Melt the remaining 2 tablespoons of butter. Pour the butter into the crushed crackers and stir to combine.
Sprinkle the crackers over the layer of shredded cheese in the casserole.
Bake for 15-20 minutes until cheese has melted and crackers are golden brown.
Sprinkle with chives. Let stand for 5 minutes, then serve.