The scene that's used for the Pencil of Doom is in the middle of the Original Bunker Scene, where Burgdorf rapidly talks to Hitler about how his rant against the generals are outrageous, but Hitler claims the generals are the scum of the German people, then throws the pencils against the map in anger. In the Pencil of Doom segments, it's edited so that Burgdorf tells Hitler not to throw the pencil, but he says he will and aims at his target, using the pencils to harm them.