1. Preheat oven to 400 degrees F and brush your squash with 1/2 tbsp olive and oil, sprinkle with salt and pepper and place on a large baking sheet.
2. Bake for about 40 minutes, or until fork tender. Set aside.
3. In a large skillet, heat 1/2 tbsp olive oil over medium-high heat. Add onion, garlic, and red pepper and cook for about 5-7 minutes, or until vegetables are soft.
4. Add ground soy, 1/2 tbsp each oregano and basil, red pepper flakes, canned tomatoes, balsamic vinegar. Bring to a boil and reduce heat to medium and simmer for about 5-10 minutes, or until thickened.
5. Meanwhile, in a small bowl combine cottage cheese and remaining oregano and basil. Season with salt and pepper.
6. Fluff up some of the strands of the spaghetti squash and divide the cottage cheese mixture evenly among the squash halves. Cover evenly with the sauce and then the shredded cheese.
7. Bake at 400 for about 10-20 minutes, or until cheese is bubbly and browned.