Cut the squash in horizontally. Cut a flat spot on the bottom so the squash stay upright while baking. Using a spoon, scrape out the seeds. Brush with olive oil, sprinkle with a little salt and pepper and place on a baking sheet. Roast for 30 minutes or until fork tender. Keep oven on.
While the squash roast, prepared the filling and topping.
Cook the quinoa according to the package directions.
Heat 1 tablespoon of oil with the butter in a small skillet over medium heat. Add the breadcrumbs and cook, stirring frequently, until golden brown, about 5 minutes. Combine in a small bowl with the Parmesan cheese.
Heat 1 tablespoon of olive oil in a large skillet over medium-high heat. Add the onion and apple and cook until softened, about 5 minutes. Add the garlic and cook for 30 seconds. Add the sage and thyme and the cooked quinoa. Cook for another minute, stirring, to combine the flavors. Season to taste with salt and pepper.
Using a spoon, distribute the filling evenly among the baked squash. Top with the breadcrumb mixture and bake for another 15 minutes.