Can you recommend a user-friendly FTP/SSH software?

First of all, omni only supports the SSH protocol, both for login and file transfer. However, you can FTP to outside omni, using the ftp UNIX command. A list of SSH clients can be found here. IST has a campus license for the SSH Shell software, for Windows, which can be found here: http://ftp.isr.ist.utl.pt/isr/ssh/ (access restricted to ISR network).