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Installing Deluge and FlexGet headless

First go through this excellent guide to install Deluge Daemon: http://www.havetheknowhow.com/Install-the-software/Install-Deluge-Headless.html

Install FlexGet using the official guide: http://flexget.com/wiki/InstallWizard/Linux

When asked to create a configuration file, create /var/lib/deluge/.flexget/config.yml.
Then start from this example configuration file if you are using thetvdb.com:
http://flexget.com/wiki/Cookbook/Series/DelugeThetvdbSeries

If you are not using the tvdb.com you can start from the Deluge example configuration on this page:
http://flexget.com/wiki/Cookbook/Series/SimpleSeries

*Tip: If you have an already filtered feed you can use all_series instead of listing the series you want to download one by one.

You can also start from my configuration:

presets:
  tv:
    all_series: yes
    exists_series:
      - /some_path/tv
      - /some_path/incomplete
    set:
      path: /some_path/incomplete
      movedone: /some_path/%(series_name)s/s%(series_season)02d 
    deluge:
      maxupspeed: 300.0
      maxdownspeed: 200.0
      ratio: 2 
      label: tv
      removeatratio: yes

feeds:
  tvfeed:
    priority: 1
    preset: tv
    rss: RSS FEED URL 

Set the ownership of the folders in your configuration to deluge:deluge and check the config.

sudo -u deluge -H flexget --check

sudo -u deluge -H flexget --test

*Tip: FlexGet configuration documentation.

To make FlexGet run every 30 minutes add the following line to the root users crontab:

*/30 * * * * sudo -u deluge -H flexget --cron

You should now be all done. Good job!

Update
If you want to access the Deluge web UI from outside in a safer way you can use Apache's proxy module. A post about it on the Deluge forum.

*Tip: Use SSL for extra security.