It depends.
If you want to your app to work on multiple screen sizes, you make separate folders and place a separate layout for each screen size (small, normal, large, xlarge). So for one layout you have four files of the same layout in different folders.
If you want to your app to work on multiple pixel densities, you make separate folders and place a separate layout for each pixel density (ldpi, mdpi, hdpi, xhdpi). So for one layout you have four files of the same layout in different folders.
If both, then both.
But as such, I don't think there is any way to arrange the layouts INSIDE the folder.