that protractor (vnu) should remain outside your website folder.
the website folder should have in it :
files folder and html pages-(index being the homepage) and any flash gallery folders music folders etc; if you have these installed. Any documents that you have linked to will in the Download folder which is located inside the files folder. If you do not have this folder in there , VSD will make one when you link a document so don't worry about that.
Only images will be inside the files folder, and images VSD renames will also be in the files folder.
here's my structure -should be the same on your comp as on server:
http://www.kellyinfo.com/web/structure.jpg