Puree the chipotles in a small food processor until smooth. Rub each side of the steak with the chipotles and marinate in the refrigerator for 1-2 hours or on the counter for 30 minutes.

Heat oven to the lowest setting (or a warm setting, if you have one). In a large skillet, preferably cast iron, heat two tablespoons of the oil over medium-high heat. Add the onions and cook until golden but not completely caramelized, about 8 minutes. Transfer to a heat proof bowl and keep in the oven until ready to serve.

Add the remaining tablespoon of oil to the skillet and return to medium-high heat. When the oil is hot, place the steak in the skillet and cook to your desired doneness, about 3 minutes per side for medium-rare skirt steak and 5 minutes per side for medium-rare flank steak. Remove from skillet and allow the meat to rest for at least 5 minutes. Slice against the grain and toss with the onions. Taste for seasoning and add salt if needed. Serve with the warmed tortillas, goat cheese and salsa.