How can I make automatic payments optional?

I think you could ask your users if he wants to pay online, based on the answer you could show/hide the payment section, do note that the payment will not be processed if the payment section is hidden. 

Here is a guide that will help you showing/hiding fields: https://www.jotform.com/help/316-How-to-Show-or-Hide-Fields-Base-on-User-s-Answer 

You would also need to set hidden fields to be cleared, this can be done under the form settings: 

You could also provide us more details about what you would like to achieve as well as the form you're working on, we will be glad to help you.