No, you do have to upload those files to the vbulletin folder.
So for example, your gallery url would look like this, http://www.yoursite.com/forums/gallery/
any file in the downloaded folder that's in the /forums folder should be uploaded in the vbulletin folder. As far as the gallery files, you can upload them anywhere you want and rename the folder.
Don't worry about overwritting anything in the vbulletin folder. If this is a fresh install, you wont have to overwrite anything as the filenames are different than vbulletin files.
hope that helped.