Preheat oven to 400 degrees.
Season the chicken thighs with salt and pepper on both sides.
Place a large skillet with olive oil over high heat and let the oil heat for a moment. Add the chicken to the skillet and sear the chicken on both sides for 3 minutes each so that each side is golden brown. Add the salsa to the skillet and cover the skillet with a tight fitting lid. Reduce the heat to medium and let the chicken cook for 25-30 minutes. After 20 minutes, using a pair of tongs, flip the chicken over to the over side and continue to cook for another 10 minutes. Turn the heat off and using 2 forks, shred the chicken.
Meanwhile cut tomatillos in half and lay, cut side up, on a baking sheet. Drizzle with olive oil and roast for 10 minutes, or until soft. Remove and let cool.
In a food processor or blender combine tomatillos, cilantro, onion, jalapeño and garlic. Pulse until smooth. Season with salt and pepper. Scoop two large spoonfuls of chicken into each tortilla and top with as much cheese as desired. Roll the tortillas and place, seam side down, in a prepared baking dish. Turn oven temperature down to 375. Pour green sauce over enchiladas. Cover with aluminum and bake for 20-30 minutes. Remove and top with chopped red onion and fresh cilantro leaves.