Preheat the oven to 350°F
Pierce the squash with a fork in several places. Microwave on high for 12 minutes, rotating at least once. Let the squash cool, then cut in half, lengthwise, and scoop out the seeds with a spoon. Scoop out the flesh into a large bowl. Add zucchini, onions and tomato sauce. Season with salt and pepper. Spoon the mixture into a three-quart shallow baking pan. Bake for 40 to 45 minutes.
Remove the baking pan from the oven and turn the oven to broil. Top the casserole with the grated cheese and place under the broiler until golden brown, about 5 minutes. Let sit for 5-10 minutes before serving.
To make the caramelized onions: (makes two cups)
1 tablespoon expeller-pressed canola oil
3 large onions, thinly sliced
Heat canola oil in a large nonstick skillet over low heat. Add the onions and cook for 30 minutes, stirring often, until soft and brown. Let cool and store in a covered container in the refrigerator for up to three days.