Heat oven to 350°F. Heat oil in medium sauté pan over medium-high heat. Add onions; cook until soft and translucent, about 5 minutes. Add chorizo; cook until lightly browned, about 2 minutes. Add jalapeño pepper and garlic, cook until fragrant, about 1 minute more. Stir in chipotle sauce; remove from heat.
Meanwhile, fill 9”x13” glass baking dish halfway with water. Place 8”x8” glass baking dish inside to create a bain marie. Place shredded cheese in smaller dish. Top cheese with chorizo mixture; cover tightly with aluminum foil.
Bake until cheese melts, about 10 minutes. Serve hot, with warm tortillas.
For cheese that’s smooth and gooey (not burnt or oily), we bake the Queso Fundido in a make-shift bain marie. This way, the water diffuses the direct heat of the oven, helping the cheese melt softly and evenly. If you want the same results without turning on your oven, simply cook the cheese in a stove-top double boiler. To do, fill a medium pot with 3” of water, simmer and set a heat-proof bowl on top (making sure the bottom of the bowl doesn’t touch the water.) Then, stir in the cheese and the cooked chorizo mixture, and heat until melted.