Start by boiling the manicotti shells according to the package instructions. Ensure that they are al dente, as they will continue to cook in the oven. Once cooked, drain and set aside to cool slightly.
In a large skillet, melt the butter over medium heat. Add the chopped onion, minced garlic, and jalapeño peppers. Sauté until the onion is translucent and fragrant, about 5 minutes.
In a mixing bowl, combine the sautéed onion mixture with the shredded chicken, cream cheese, sour cream, and 1 cup of salsa. Mix until well combined and creamy.
Using a spoon or a piping bag, carefully fill each manicotti shell with the chicken mixture. Be generous but gentle to avoid breaking the shells.
Spread a thin layer of enchilada sauce on the bottom of a baking dish. This will prevent the manicotti from sticking and add extra flavor.
Place the stuffed manicotti shells in the baking dish. Pour the remaining salsa over the top, followed by the enchilada sauce. Sprinkle the Monterey Jack, cheddar, and Parmesan cheese evenly over the top.
Preheat your oven to 350°F (175°C) and bake the manicotti for 25-30 minutes, or until the cheese is melted and bubbly. For an extra touch, broil for an additional 2-3 minutes to get that beautiful golden top.