Again, this part of the process needs to be done by someone with access to the server.
Now, you can upload files of any size into the directories. You would use an FTP client such as FileZilla, Fetch, or WinSCP:
To determine the correct permissions for the repository files, look at the permissions for the files under filedir, which is also in the Moodle data directory. Duplicate those permissions for the files that you upload into your repositories.