Since you feel rest of your script is all done, here is the FTP command related code:
%WinScpDirectory%\WinSCP.com /script="ftp.txt" /log="FtpLog.log"
put the following code in ftp.txt file and place the file in the same folder as your script file (or where ever you want to, but keep the path if you choose to have it in a different folder)
option echo on
option batch on
option confirm off
open username:
[email protected] -hostkey="ssh-rsa 1024 11:22:33:44:55:66:77:88:99:11:22:33:44:55:66"
cd /fromlee
put C:\encryptedfiles\*.*
close
exit