If you try to set the Directory path up from the application root folder like this ...
FileManager1.RootDirectories(0).DirectoryPath = Server.MapPath("../../FilesFolder")
The following error occurs
"Cannot use a leading .. to exit above the top directory"
However there is a work around by setting the path as follows:
FileManager1.RootDirectories(0).DirectoryPath = Server.MapPath("") & "..\..\FilesFolder"
By counting the levels deep the app path is it should be possible to set the root folder to any other folder on the same drive as the application.
**** Note this does not seem to work in VS2008 Cassini web server - but does work under IIS 6 (haven't tried IIS7)