It means upload all the files in the uploads folder to your forum root directory. aka your forum folder on your web server.
example: if
http://www.domain.com/forum/ <-- = URL in coding terms
usr/httpdocs/forum/ <-- = PATH..
c:\network\apache2\httpdocs\forum\ <-- = PATH
when you upload to the root of a directory it means your uploading the contents of the uploads directory to the begining of the specified directory.
In this case, your forum root, so if you FTP to your server you would follow the PATH to where your forum folder is located on your server, and upload the files there.