The area you are referring to is for setting CONDITIONALS
Using the Shortcodes in Display Settings.
The application template is set-up with default settings as soon as the plugin is activated.
This setting allows you to define the template for displaying the application form. If you’re happy with the current application form, just leave this blank, as you’ll need to update it each time you add a new field to the application form.
If you want to modify – add or delete form fields you do this via the App Form Settings Tab.
More information Customizing the form can be found here
Styling of the form is via your default theme or by adding the display css from Job Manager to your themes style sheet.
Hope this helps.