Editroid's map, or the "editor map," uses color coding to indicate which level each screen belongs to. But this information is not taken from the ROM, since this information is not contained in the ROM in the first place. Editroid can not infer which level each screen belongs to. The first time you load a ROM, Editroid guesses which level each screen belongs to. If it guesses wrong, you need to make the necessary corrections to the editor map. Every time you save the ROM, the editor map is saved along-side the ROM data.
Simply changing the colors on the editor map will not necessarily have any change in the game, and it is very possible to make the map in the editor to show something different from what will be seen in the game. When a room is added to the map, the level it will belong to should be marked on the editor so that the editor will know which level's data to use when the screen is displayed and edited. It is also important to remove a screen from the editor map if it will no longer be used, in order to maintain organization.
Screens that appear black in color on the map are marked in the game data as inactive. During game play, the screen will not scroll into these rooms. If an unobstructed path leads to an inactive screen then the player can walk off the edge of the screen and will not be able to see Samus (and, most likely, won't be able to get back into the visible part of the level).
How To Use The Map Editor