To make the pumpkin filling for the pasta, begin by melting ½ cup butter in a large skillet, and saute diced onion, sage, and thyme over medium heat until the onion is softened and translucent.
Add the pumpkin purée, salt, peper, cream, and brown sugar to the pan. Stir to combine and heat through. Remove from heat and set pasta filling aside.
To make the burnt butter and sage sauce, melt ¾ cup of butter over medium-high heat in a medium sauce pan. Once the butter is melted and begins to foam add 24 whole sage leaves. Let the butter brown. Remove it from the heat when it begins to smell nutty, but isn't burnt black.
To prepare the manicotti noodles, boil it in a large pot of salted water until it's tender, according to the recommended cooking time on the package instructions. Unlike some stuffed pasta, this dish doesn't really get more cooking in the oven -just heated through, so make boil your pasta until it's as tender as you like to eat it, and then drain pasta shells.
Once pumpkin filling is slightly cooled, add to a piping bag and use it to fill the cooked pasta tubes.
Layer filled pasta in a large baking dish, and pour the sage browned butter sauce over it the top of the manicotti, and between layers.
Lastly heat the pasta dish in a preheated oven at 350 until the manicotti is heated through, around 15 minutes, and enjoy.