Set the External Resource Location to the relative subdirectory to which you want your files written at build time. This subdirectory will be created on the specified External Resource Media ID, and the files are placed in that subdirectory during the build.

NOTE: This property is ignored if the Stored As property is not "External Resources".

For example, the preview of your Files bean is as follows:
    data/config.txt
    data/fileset1/readme.txt
    data/fileset1/eula.html
    data/fileset2/abc.txt
and you've set
    Stored As = "External Resources"
    External Resource Location = "myfiles/extras"
    External Resource Media ID = 1
Then, after building your project, your "disk1" directory contains:
    disk1/myfiles/extras/data/config.txt
    disk1/myfiles/extras/data/fileset1/readme.txt
    disk1/myfiles/extras/data/fileset1/eula.html
    disk1/myfiles/extras/data/fileset2/abc.txt