Disable authentication by stopping daemon (sudo service transmission-daemon stop) and setting transmission-daemon --no-auth (this is just the quick and dirty way to get started remotely; you should probably use proper auth for actual config).
Set the target directory with transmission-daemon --download-dir /path/to/dir
Start the daemon back up sudo service transmission-daemon start
Go grab a magnet link and run transmission-remote -a "<magnet-link>" to start a torrent download (should receive a “success” message if started correctly)
Check on the status of downloads with transmission-remote -l (optionally prefix with watch)