All uploading clients should automatically be in the correct folder after they connect. Do not change your software's default upload directory setting unless you are absolutely sure your client is getting it wrong.
For FTP clients (including publishing programs such as Dreamweaver that upload using FTP), the correct directory is /public.
For ssh and SFTP clients, the correct directory is /home/public.
(Once uploaded, scripts that run on your site will use a different path to access your files, depending on whether they are PHP or CGI.)