Can the ftp accounts be configured to use either SSH or SSL encryption for file transfers? I am thinking of moving a site that currently uses SSH for the FTP server and just want to make sure I can set that up here as well.

You can use http://winscp.vse.cz/eng/. It works either through ssh or ftps to securily transfer files and works when one of this avaliable. You can use it with our servers.

I already have WS FTP Pro as my ftp client. Can I continue to use this client instead of the other one you listed in your response?

Yes you can continue to use it as your FTP client with our servers. WS WTP also supports secure connections via SFTP/SSH.