transmission-daemon accepts a watch_dir option to watch for incoming .torrent files. See: https://trac.transmissionbt.com/wiki/EditConfigFiles#FilesandLocations
It'd be nice to include those options in the config template. I've added those in a fork at https://github.com/jamesdabbs/transmission (master) and will open a pull request momentarily.
First time contributing; let me know if I messed up the process anywhere.