Plugins are the difference between flat and dynamic templates.
Plugins are used to modify a template specifically for the end user by inserting logos, updating addresses, applying color themes etc.
Plugins are configured by super admins. As an admin, you can add already existing plugins to templates.
Plugins are added in the 'File editor'. Simply choose a plugin from the drop down list, and click add.
The plugin is then run automatically in end back end when the template is downloaded.