These auto-fields are also available for the subject of the email. Click on the text in the subject to find the auto-fields on the left.
When entering text, click on 'Merge Tags' to select these auto-fields.
Once you have applied the changes, close the screen using the cross in the top right corner. The changes are automatically saved here or click [Save as] to save this as a new template.
Certain email templates must still be selected in the corresponding setting to be used as a default email. For example, for Finances, this is set in Settings -> Finances -> Invoicing -> Print & mail.