How can I have an auto receipt sent to the person filling our my form, paying an application fee?

When you add an email field to your form an email auto-responder is also added to it; however, you could also manually add an email auto-responder to your form by following this guide: https://www.jotform.com/help/26-Setting-Up-an-Autoresponder-Email 

If you have any question, please let us know.