Preheat oven to 450 degrees. Rub potatoes with oil and pierce with a fork on the top of each potato six times. Place on a foil lined baking sheet. Bake for 45 minutes to 1 hour or until the internal temperature reaches 200 degrees F.
Meanwhile, in a medium skillet set over medium low heat, add 2 tablespoons of butter. Once the butter has melted add the onion. Sprinkle with salt and sugar. Cook until caramelized, about 30 minutes. Stir frequently to prevent burning.
Add the pepper and garlic. Cook for 2 minutes or until the garlic is fragrant. Pour in beef stock and thyme. Turn to medium heat and simmer for 15 minutes.
Remove the potatoes from the oven and cut down the center with a knife. Press the ends together to pop the potato open (just be gentle). Divide the remaining butter into 4 pieces. Place into the center of each potato. Carefully ladle the soup into each potato, dividing evenly between the two. Go back and forth to allow as much liquid to be absorbed as possible.
Place a slice of cheese over top and broil until cheese is golden brown. Remove from the oven and serve.