Preheat the oven to 400 degrees.
Place the squash on a sheet pan, add 2 tablespoons olive oil, the cinnamon and ½ teaspoon salt and toss lightly with your hands. Roast for 30-35 minutes, until tender, tossing twice during cooking with a metal spatula so the cubes brown evenly. Set aside the squash and the pan.
Meanwhile, heat 1 tablespoon of the butter and the remaining 2 tablespoons of the olive oil in a large (12-inch) sauté pan over medium heat. Add the onions and cover for 10 minutes to let them steam. Remove the lid and continue to cook over medium-low heat, stirring occasionally, for about 45 minutes, until the onions are caramelized and golden brown. If the onions are cooking too fast, lower the heat. Add the vinegar and ½ teaspoon salt and cook for 2 more minutes, scraping the brown bits from the pan. Remove from the heat and set aside.
Place the cooked squash in the bowl of a food processor. Add the chipotle pepper, maple syrup, chicken broth, the remaining 2 tablespoons butter, and 1/2 teaspoon salt and process until smooth. If the puree seems very thick (this will depend on the size of your squash) add an additional 1/4 cup chicken stock.
Spread one layer of chips onto the sheet pan you used to roast the squash. Spoon half the squash mixture on top, distributing it as evenly as you can. Spoon half the caramelized onions on top, followed by half the Fontina and half the Monterey Jack. Repeat with remaining chips, squash, onions and cheese to make one more layer. Bake for 10 minutes, until the cheese has melted and is beginning to brown at the edges.Sprinkle with the avocado and pepitas and serve!Copyright 2016, Lidey Heuck, All Rights Reserved