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Are all users transferring their files to the same directory or is File Transfer user-based?

Every user has his own User Zone.
In case of the push method (SFTP/FTP) he will not see the directories of the other users.
In case of the get method (connection from application server to User Zone via SFTP) currently the user can browse through the directories with the cd command.

Where does FileTransfer backup the files that are transferred? Who has access to these files and is the length of time in which these files are stored configurable?

Like the films, the files are stored in Sessionstore and they are also encrypted. Every user, who is able to use Management Desk, configured with the according role has access to the files.
The files also have a lifetime which is configurable.

end faq