Preheat your oven to 375°F (190°C).
In a large bowl, combine the sliced yellow squash, salt, and black pepper. Toss to coat the squash evenly.
In a separate bowl, mix together the cheddar cheese, Parmesan cheese, breadcrumbs, olive oil, garlic powder, oregano, and red pepper flakes until well combined.
In a greased 9x13-inch baking dish, layer half of the seasoned squash slices evenly across the bottom.
Sprinkle half of the cheese and breadcrumb mixture over the first layer of squash.
Add the remaining squash slices on top, followed by the rest of the cheese and breadcrumb mixture.
Cover the baking dish with aluminum foil and bake for 25 minutes.
Remove the foil and bake for an additional 15-20 minutes, or until the top is golden brown and the squash is tender.
Let it cool for a few minutes before serving.