I have two 'web' directories, which do I use?

Each site has a master web directory and each user within that site has their own sub directory...

TypeFull PathFTP PathURL
Site/home/sites/www.example.com/web/webhttp://www.example.com
User/home/sites/www.example.com/users/username/web/users/username/webhttp://www.example.com/~username

...obviously only users set up as site admins can put things in the site directory.