...I used wsftp...
SME ibays contain three folders by default:
/home/e-smith/files/ibays/<ibayname>/files
/home/e-smith/files/ibays/<ibayname>/cgi-bin
/home/e-smith/files/ibays/<ibayname>/html
FTP and Samba access the .../files folder - which is (by design) not available from the web.
Apache uses the files in .../html (and sometimes .../cgi-bin).
If you have only examined your system using "wsftp", you would not be able to see the html or php files in the .../html folder.
You need to download, install, and figure out how to use WinSCP (
http://winscp.net/eng/download.php), which uses ssh to connect to your SME server, but then gives you a file manager interface to allow you to easily copy files from windows to the .../html folder (or any other folder) on your SME.