Preheat the oven to 350 degrees and spray an 8x8 baking dish with nonstick cooking spray.
Cut the squash into 1/4 inch slices. (you don't want them any thinner then that or they will get to mushy)
Heat a large skillet on medium high heat and add 2 tablespoons of butter, add in the sliced squash and diced onion and cook just until soft about 8 minutes. Then add in the minced garlic and cook another 30 seconds and remove from the heat.
Add the cooked squash to a colander and give it a few stirs to remove as much of the liquid as possible. Let that drain for about 10 minutes.
In a small bowl, add the mayonnaise, sour cream, milk, eggs, parmesan cheese, colby cheese, cayenne, salt, pepper, and thyme and mix until combined.
In another small bowl, add the crushed crackers and mix in the melted butter until crackers are coated.
Add 1/3 of the sauce to the bottom of an 8x8 casserole dish, followed by 1/2 of squash, another 1/3 of the sauce, the remaining squash, and then the remaining sauce.
Spread the crushed crackers over the top.
Bake for 25-30 minutes or until golden brown and cooked through.
Notes
Any buttery cracker will work fine.
Store leftovers in an airtight container in the refrigerator for 3-4 days.