Do you have webhooks?

I need to use webhooks, to send my data back to our application, so using encryption will not work.  Do you have, or are you planning on adding a feature that will encrypt the data at rest.  Using https and having the data encrypted at rest would be secure enough.

Yes, you can integrate web hooks to your forms.

Here is a  guide on how to set it up. How-to-Setup-a-Webhook-with-JotForm

All forms in JotForm are already secure by default, you can read the article here: All-Forms-Including-Free-Accounts-Are-Now-Secure

I hope this information helps.

I know I can use webhooks.

I also know that when I submit data, it uses https.

Both of these are great, and work.

When my data is stored in jotforms servers, is it encrypted?  I can not use the system that encrypts data while the form is submitted because my webhook would not longer work.

Yes, the data is encrypted in nature. This is for the security. The data is also encrypted during the transmission, considering the form uses HTTPs. 

Note the encryption as per this guide (https://www.jotform.com/help/344-What-are-Encrypted-Forms-and-how-to-use-them-as-expert) is different from the server side encryption. This feature is to add an extra layer of security. When enabled, only you can view your form data as the form will need you to provide the encryption key. Other features such as the integrations, so with Webhook are automatically disabled. Please read the given guide to know more about the form encryption.