Has it been a while since you used FTP from the command line? While there are decent GUI-based FTP clients (such as gFTP), you can automate operations with the command-line version and handle file transfers with no user interaction at all.
When you try connecting to an FTP server and specify a username, FTP won't do anything unless you type in your password, or specify it in the connection command, as in
ftp bainm:firstname.lastname@example.org. You can take advantage of this syntax to automate your FTP transfers using a pipe: