Bring a large pot of salted water to boil and add in the zucchini and squash and cook for about 10 minutes, until tender. Drain and arrange in a greased 3 quart casserole dish. Set aside.
To another large pan, melt the butter over medium heat. Whisk in the flour and cook about 1 minute. Gradually whisk in the heavy cream, until the mixture begins to thicken. Stir in the garlic and parmesan cheese and season with salt, pepper and red pepper flakes.
Pour the creamy, cheesy mixture over the zucchini and bake for 15 to 20 minutes, until the center is nice and bubbly. Enjoy!