Preheat oven to 350℉. Sprinkle the bottom of a 9x13 inch baking dish with breadcrumbs or almond flour.
In a 9x13 inch baking dish, toss together zucchini, yellow squash, scallions, dill, feta, 1 cup mozzarella, parmesan, salt and pepper. Evenly spread this out in the dish and bake for 40-45 minutes. Remove from the oven and top with the remaining shredded cheese and bake for another few minutes or until melted.