Prepare the sauce: Preheat the oven to 425°F. Place the diced butternut squash, onion, and whole garlic cloves on a sheet pan. Drizzle with olive oil, salt, and pepper. Toss to coat. Roast for 20-25 minutes, tossing halfway through, until squash is tender. Once vegetables have roasted, reduce oven heat to 375°F (for baking the stuffed shells). Place the vegetables in a blender (or a large stockpot if immersion blending) along with the vegetable stock. Leave some diced if looking for a chunkier sauce. Place the blender lid on top, cracking the top hole a bit to allow steam to escape. Puree ingredients together, blending until smooth. Add additional stock if needed. Taste and adjust for salt levels. 

In a large saucepan or skillet, over medium low heat, melt the butter. Add the shallots and the garlic to the melted butter and cook, stirring for 2 minutes. Do not let them brown.

Add the flour and stir. Cook, stirring constantly for 1 minute. Add the vegetable broth and blended squash alternately. Stir constantly so the mixture is smooth. Add the milk and continue stirring. Raise the heat to medium and stir until the mixture bubbles and thickens. Add the nutmeg, salt, pepper and brown sugar. Stir well. Add the butternut puree and stir until mixed in well and warm.

Shells: Meanwhile, bring a large stockpot of salted water to a boil. Cook the jumbo shells for half of the recommended cook time. Drain and rinse. Set aside.

Filling: As the shells cook, prepare the filling by mixing together all the filling ingredients (cheeses, minced garlic, and dried spices/herbs). Taste test and adjust salt levels as needed. Set aside.

Assembly: Spread 2 cups of the sauce on the bottom of an 8×8 or 9×9 ceramic or glass baking dish. Take a shell and scoop or pipe approximately 2 Tablespoon of filling inside of it, placing it on top of the sauce in the baking dish. Continue filling each shell until finished. Top the shells with the remaining 1 cup of sauce. Sprinkle additional cheese on top as desired.

Baking: In the 375°F oven, bake for 26-30 minutes until golden brown and bubbly. Remove and let cool slightly before serving.

Crispy Sage: While the pasta bakes, melt 1 Tablespoon  butter in a small skillet over medium-high heat. Add the sage leaves, and using a fork, turn occasionally as they crisp up in the butter for 2-4 minutes. Once they're crispy and deep green in color, remove with the fork and place on a paper towel until ready to serve. Garnish baked pasta with the crispy sage.