Bring a large pot of salted water to a vigorous boil. Add the jumbo shells and cook until just firm to the bite, following the package’s suggested time. Drain thoroughly, then place the cooked shells on a baking sheet in a single layer to keep them from sticking together.
Place a skillet over medium heat and cook the ground meat with the finely chopped onion, breaking up the meat as it browns. Once the mixture is cooked through and no longer pink, drain off any rendered fat.
Stir in the taco seasoning and measured water, mixing thoroughly. Let the mixture simmer for about 3 to 4 minutes, stirring now and then, until slightly thickened. Incorporate the drained tomatoes with green chilies and half of the salsa. Take the pan off the heat.
Preheat the oven to 375°F (190°C). Prepare a 9x13-inch baking dish by coating it lightly with cooking spray or oil. Spread the remaining half cup of salsa evenly along the bottom of the dish.
Fill each pasta shell with approximately 1 to 2 tablespoons of the seasoned meat mixture. Arrange the stuffed shells snugly in the prepared dish.
Scatter the shredded cheddar and Monterey Jack cheeses evenly over the shells. Cover the dish with foil and place it in the oven for 20 minutes. Uncover and continue baking for another 5 minutes, or until the cheese topping is thoroughly melted and bubbling.
Allow the dish to rest for about 5 minutes before serving. Garnish with sour cream, chopped green onions, and cilantro, if desired. Serve while hot.