Email Notification upon PTO Status Approval or Non-Approval

I created a PTO Request Form (Time Off Request) and have set up email notifications and auto-responders with conditions based on the Supervisor field.  When employees submit their form they get a notification email from the Supervisor and the Supervisor gets a notification email with their request.  Once the supervisor goes into the form to edit the PTO Status field to either Approved or Not Approved and clicks submit - the Supervisor is getting another email with the updated form showing the status filled in, which is correct, but the email is coming from the form submitter instead of the Supervisor and I also cannot get an email to go back to the submitter once the PTO status field has been updated.  I need help!

This is what I understand from your post.

1. You would like your form users to make submissions to your PTO Request Form
2. Notifications are being sent to the supervisor (Notifier) and to the user who submitted the form (Auto Responder) for the initial submission.
3. When the supervisor reviews the submission and decides if it is approved or not and make the necessary changes, a notification would only be sent to the supervisors email but not the form user's email.

Is this correct?

I believe you would like the form user to get a notification once changes were made to the submission but that is not how the auto responder works. It will only sends notification on the initial submission. All later amendments is only sent to the administrator (supervisor) of the form.

With the use of Mandril, you can set the form user's email as the From field so that the supervisor can simply reply to the email with the PTO status whether approved or not. 

You can review how it works here:
http://www.jotform.com/help/236-How-to-use-Mandrill-to-Send-Emails-From-Your-Own-Email-Address 

I hope this information was useful. Please advise us if further assistance is needed.

Cheers!