How to notify user if his submission was denied.

is there a way when going through submissions that if a submission is not accepted to to notify the notification e-mail? 

That is possible. You can setup an autoresponder, which can be triggered through conditions, if the application is denied.

We have created a general guide that covers how to build a basic approval workflow form, please check it: https://www.jotform.com/help/432-A-General-Approach-on-Building-an-Approval-Process-Workflow