Editing Levels question

The map index sets which NPCs are on screen, dictates the random encounter table (and if there are random encounters or not), and handles on-entry event triggering.

Several maps share the same TILEMAP, though, which is why adding a chair to Figaro Castle Basement adds that chair to every map that uses the basement tilemap. This was done by the original FF6 development team to save space. It is to such an extreme that even rooms with completely different tilesets occur on the same map, such as the Magitek Research Factory's tube rooms (which look garbled when looking at the factory floor, and vice-versa).

The only way around it is to expand the ROM and make new maps from scratch; I can't help you with that personally but FF6LE Rogue CE is supposed to be able to handle map expansion. Beware of byte 17; it handles how the tilemap decides priority and should match whatever value the original map with that tileset had. I know there was an issue with that value not saving on Rogue CE, but I do not know if that bug has been corrected on the wiki version.