Drizzle acorn squash halves with ½ tablespoon olive oil per squash half. Sprinkle with a generous pinch of salt and pepper. Roast for 45 minutes, or until the squash is fork tender.
While the squash is cooking, heat a large sauté pan with 1 tablespoon of olive oil. Add the sausage and brown. Add the onion, celery, garlic, red pepper flakes, and a pinch of salt and pepper. Cook for 3-4 minutes, or until the onion is tender and translucent.
Remove the pan from the heat and stir in the chopped thyme and rosemary. Stir in the quinoa, apples, and dried cranberries. Season with salt and pepper to taste.
Scoop the mixture into the roasted acorn squash halves. Top with parmesan cheese and a drizzle of olive oil. Bake for 10 minutes.