yes you need to have 2 layouts, 1 for the map or the topdownview like you say, and 1 for the sidescrooling area /dungeon,
you can also do it in the same layout, on different layers, however it will be to complicated and probably youl get confused at some point in development when stuff will be to crowded, but the same layout suggestion ,i dont think is recommended since all the objects wold be present there and the resources utilisation wold explode.