I'm a bit confused by what you mean with the directory doesn't "show". Anyway, you can use any FTP program (Winscp, Filezilla) to view your root directory and see what your directory structure looks like and also view your associated permissions.
All directories start with root and other directories are at a sibling or child level. To reference the current directory use a period . To move up a directory use .. To move to a sibling simply reference the name of the directory ./siblingdirectory/myfile.php