Preheat oven to 400 degrees.
To make zucchini boats: Cut zucchini in half lengthwise. Place on a microwave-safe plate and heat in the microwave for 2 minutes, to soften a little. Using a spoon or melon baller, scoop out flesh. Be sure to leave ¼ inch thick inside zucchini boats. Set aside. (toss the flesh or save and add to another dish such as a stir-fry or soup).
Place 1 cup sauce in the bottom of a 9 x 9-inch baking dish. Place zucchini boats cut side up in pan. In a small bowl, add 1 cup sauce. Season with Italian seasonings and red pepper flakes and pepper. Stir in ham, pineapple, and softened onions. Mix well.
To fill zucchini boats: To each, add a rounded ¼ cup tomato sauce filling, press down to set. Top each with 1-2 tablespoons pizza sauce. Sprinkle each with 2 tablespoons mozzarella cheese and top each with 1 teaspoon Parmesan cheese. Repeat for remaining zucchini boats. Cover with foil and bake 30-35 minutes until zucchini is cooked and soft.
Be sure to use a spatula to scoop out each zucchini boats to place on each plate. Add some sauce around each boat from the bottom of the pan, if desired.