Here’s a nice post that summarizes the different flavors of the encrypted FTPS (FTP over SSL) protocol.
“FTPS is a name used to encompass a number of ways in which FTP software can perform secure file transfers. Each way involves the use of a SSL/TLS layer below the standard FTP protocol to encrypt the control and/or data channels.”
The posting then goes into a bit more of the technology details of AUTH TLS, Explicit FTPS or FTPES and Implicit FTPS…. and then SSL Certificates and some info on firewall implications.