Spray a 9x13 baking dish with non-stick spray add in the squash, zucchini, onion, oil, and seasonings stir well to coat the veggies in the oil and seasonings bake for 15 minutes.
Remove from the oven and turn the heat to 350 degrees F. Add in the remaining ingredients except for the cheese. Stir well. Cover tightly with foil. Bake for 35 minutes. Remove the foil and stir well, sprinkle cheese over the top. Bake for an additional 15 minutes or until the orzo is tender.