FXP is server-to-server FTP and using it is similar to using FTP.

1. The First thing you will need is a FTP client that supports FXP. Some examples are FlashFXP for Windows, and gFTP or kasablanca for linux.  There are plenty of free clients out there for this.
2. Connect to one seedbox in one window of your FTP client, and the other seedbox in the other window.  You can find the username and password from your information tab in your Control Panel.  Use port 21000.  You may want to 'save' or bookmark these connections so you can come back to them easily.
3. Copy the data files you want to keep in /data/[username]/rutorrent/ from seedbox to seedbox. Many clients support drag-and-drop, other require you to select the files and push the transfer button.  If you 'stop' all torrents on the from seedbox your transfers will go faster.
4. After your sure the data files are transfered, move the .torrent files related to the data you transfered in /data/[username]/rutorrent/.session/ from seedbox to seedbox.
5. Reboot the 'to' seedbox to get it to recognize the new torrent files.