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From what I gather of your details you wish to include a processing fee if the customers set of selections turns out to be above the $0 mark it seems.
This should be possible. But can you please share a link to the form you are trying to do this on so that we can get a better understanding to be able to assist you in achieving your desired workflow?
One way you could do this would be to create a calculated pricing system based on your options so that it changes the pricing if it goes above the $0 mark to then send to the payment processor.
Another option aside from that would be to create two different payment forms and show one or the other accordingly. One of them would have a required product listed on it showing your processing fee to the customer. See http://www.jotform.com/help/182-How-to-Create-a-Basic-Multiple-Payment-form to learn how to create this type of workflow as an alternative.
If you need further assistance though just let us know.