Preheat oven to 400F.
In a large sauce pan, heat the olive oil over medium heat. Add in the garlic and cook, stirring constantly, for 1 minute. Add in a pinch of salt, a pinch of black pepper, red pepper flakes, tomatoes, vinegar, minced garlic, and 1 tsp Italian Spices. Bring to a boil over high heat, and reduce the heat to simmer for 10 minutes, stirring occasionally, reducing heat if browning too quickly. Take off of heat.
In a large bowl, combine the spaghetti squash and the grated Charloe cheese and the remaining Italian spices/herbs. Set aside.
To make gratins, start with one layer of the spaghetti squash-cheese mixture into each of 4 medium ramekins, or other small oven-safe bakeware. Top each with a ladle full of the tomato sauce. Sprinkle the parmesan cheese evenly among the tops of each ramekin, spreading the cheese to the edges. Cover with aluminum foil, and bake for 35 minutes. Uncover, and bake or broil for an additional 5-7 minutes, or until golden and bubbling. Serve warm.