Usually FM and Backup automatically use IE's proxy settings, so you don't need to configure proxy settings as long as you can use IE to access DriveHQ.com. However, it seems if your proxy server requires authentication, then there is a problem here. We will look into this problem and fix it in a later version.
In the meantime, you can try third party FTP client software that supports Proxy servers. Our FTP server info is available at: http://www.drivehq.com/ftp/
You might be able to use IE as an FTP client, try: