Preheat oven to 400 degrees F.
Boil manicotti in salted water for 8 minutes. Drain, reserving 1/2 cup of pasta water and set pasta aside.
In a large skillet, heat oil over medium heat. Saute onion until translucent, about 3 minutes. Add garlic and saute 1 minute more. Remove pan from heat and mix in chicken, tomatoes, cilantro and sour cream. Set aside.
Place tomatillos, onion, jalapeno and garlic in a baking dish. Toss with oil and season with salt and pepper. Roast until tomatillos turn golden around the edges and are soft, about 45 minutes. Remove from oven and blend ingredients together until smooth. Use reserved pasta water to thin sauce, if necessary. Season with salt and pepper, to taste.
To make the cheese sauce: In a medium saucepan, melt butter over medium-high heat. Add flour and cook 2 minutes. Whisk in heavy cream and bring to a simmer. Add cheese and nutmeg and stir until melted. Season sauce with salt, to taste.
To assemble: Reduce oven temperature to 350 degrees F. Stuff manicotti tubes with chicken mixture and assemble in a 9 by 12-inch baking dish. Pour cheese sauce over the top. Bake 30 minutes until cheese is bubbling. Drizzle tomatillo sauce on Maniladas before serving.