Preheat the oven to 375º. Grab a large skillet and heat the oil on medium/high heat.
Heat up the butternut squash, if using frozen, put it in the microwave for about half the time the package calls for to soften them up. If you have fresh roasted squash, skip this step!
Add chopped onions to the skillet, start with the onions. Sauté for about 2 minutes. Next add in the seasonings, beans, tomatoes, chipotle peppers, squash.
Sauté on medium heat for about 4-6 minutes, until the seasonings are fragrant feel free to mash everything together just a bit so it fits into the tortillas better. Take it off the heat and prepare the vegetarian enchiladas.
Grab a large baking dish, put about 1/4 cup of red enchilada sauce on the bottom (this helps everything from sticking to the baking dish). 
Gently roll up the enchiladas. Try not to over stuff them, otherwise they can crack. Snuggle them up into the baking dish.
Once they are all ready and stuffed, pour the leftover enchilada sauce over the rolled tortillas and sprinkle well with shredded cheese. Bake for about 20 minutes or until the cheese is melted, and the sauce is bubbling. Garnish with chopped cilantro. Serve with your favorite toppings and enjoy!