Doomedit is pretty old and buggy, Dark Radiant is a much better level editor for Doom 3, as well as numerous other games on this engine. I haven't experienced any errors with it so far and it's quite easy to use. Giving it a path to your game directory is the only necessary configuration, the editor handles all the rest on it's own.
You can download it from this page.
You can download it from this page.