Here's how I've configured my Flexget install:

In ~/.flexget/config.yml:

presets:
  global:
    email:
      active: true
      from: siteowner@example.com
      to: user@example.com
    transmission:
      host: localhost
      port: 9091
      removewhendone: true
      ratio: 1.0
  movies:
    download: /path/to/Movies/  
  tv:
    series:
      settings:
        hdtv:
          quality: hdtv
          timeframe: 2 hours
          set:
            path: /path/to/TV/%(series_name)s/S%(series_season).02d
        720p:
          quality: 720p
          timeframe: 2 hours
          set:
            path: /path/to/TV/%(series_name)s/S%(series_season).02d
        480p:
          quality: 480p
          timeframe: 2 hours
          set:
            path: /path/to/TV/%(series_name)s/S%(series_season).02d
      hdtv:
        - Series Name 1
        - Series Name 2
      480p:
        - Another Series Name
feeds:
  ezrss:
    rss: http://www.ezrss.it/feed/
    preset: tv

Make sure to change the email settings, feed settings, and show list!

And I have this line in my crontab: @hourly /usr/local/bin/flexget -v --cron > /home/<username>/log/flexget.log

Make sure to replace <username> with your own user name!