Transmit has a great synchronize feature. But it only works with one FTP server at a time, with a folder in the Finder. Here is how to make it synchronize two FTP servers...
In Transmit, open one of the FTP server you want to synchronize. Then in Finder, under the Go menu choose Connect To Server. Mount the other FTP server with the address ftp://user:pass@server.com (fill in the details).
In Transmit, you can now synchronize the two FTP servers, since one of them is mounted in the Finder! No more using your hard drive as a swap space. The only caveat is that Finder's FTP mounts are read-only. So your synchronize is a one way street with this method. OK another caveat -- Finder's FTP speed is very slow.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20061218072232444