Ok, heres how it goes, lets assume you have
http://yoursite.com/forums/
Your forum root folder is /forums/ (sometimes it may appears like public_html/forums. or httpdocs/forums/)
If a modification says upload the files to the forum root, in your ftp program, simply drag all the files and drop them over to the side where you have your forum root folder opened.
Thats all there is to it, you dont need to do each folder one at a time, and if your missing the folder, then simply proceed as instructed above with dragging and dropping the contents of the modification into the forum root and it will be created for you.