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We currently only offer the ability for one time payments or subscriptions with equal amounts for each period.
What you could do is set up a second form to pay a custom amount for the remainder of their balance. The Custom Amount or Donation Amount is available in the Paypal Payment tool.
You can see this option available during the configuration of the Paypal payment wizard.
Refer to the screenshot below
I suggest review also this user guide http://www.jotform.com/help/49-Order-Form-Types
And here is a jotform template http://www.jotform.com/form-templates/donation-form-2 that have a basic example of the Custom Amount/Donation using Paypal tool.