Using watch directory
From Pulsed Media Wiki
This is a simple task. You only need to transfer the .torrent file into your Watch folder, and rtorrent automatically starts to download it and will download and share untill you remove the .torrent from watch folder or remove the torrent from ruTorrent webui.
Transfering the .torrent file / files to the Watch folder you need to have FTP client or use SSH file transfer.