Well, I am not sure about the newer versions of WS FTP but my version, WS-FTP 2007, supports....
FTP - This is the default setting and is the correct choice for most users.
FTP/SSL - FTP in explicit SSL mode. Encrypts the command channel.
FTP/Implicit SSL - FTP in implicit SSL mode. Encrypts the login and command channel.
Local - A local connection saves a location on your local computer or network for quick access through the Site Manager.
SFTP/SSH - Secure File Transfer Protocol. When you connect to the server, SSH will automatically be initiated. (WS_FTP Professional only)
HTTP - Hypertext Transfer Protocol. Allows you to upload or download files over the standard World Wide Web ports and protocols. (WS_FTP Professional only)
HTTPS - Secure Hypertext Transfer Protocol. Allows you to upload or download files over the standard World Wide Web ports and protocols with SSL encryption. (WS_FTP Professional only)
...you should be able to set the server type when you set up the site profile for uploadin....
You can find info on the newer version at http://www.ipswitchft.com/Individual/Products/ws_ftp_pro/?k_id=inprolinkt1