I'm not quite sure I'm following, so let me describe the way OJS treats the files directory:
When OJS is installed, you need to enter a path name into the installation form. There's a check there to make sure that the directory can be written, i.e. that file permissions are permissive enough.
After that, during regular operation of the system, OJS will create directories for each journal, and within those, each submission, in which to store submission files.
If you went through the proper installation process the directory you named during installation must already exist, and will contain subdirectories called "site" and "journals". If you later change the directory in config.inc.php, you'll need to move the directory that was previously created into its new location.
Public Knowledge Project Team