you'll be best off having the user upload one file at a time. then you'll need to use PHP server side to move the files to the right location.
if you want the users to upload a folder you might want to consider having them zip the folder up. to move the folder without zipping the folder would require the user connecting using FTP or DAV
both FTP & DAV have limited authentication options and control of what the user does. not to mention the software to connect via FTP or DAV may not be present on some platforms.