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I'm not sure if I understood your concern correctly. The IPN in the Paypal works if you have integrated a Payment Tool in your form.
Here's how you can setup an order form: http://www.jotform.com/help/165-Setting-Up-Your-First-Order-Form.
You can choose different payment processors. For the IPN for regular Paypal, when a user proceeded on doing a payment and completed it successfully in the Paypal Gateway, an email notification will be sent to you informing about it.
If you are setting a Paypal Pro IPN, you can check this guide: http://www.jotform.com/help/279-How-to-Enable-IPN-for-Paypal-Pro.
I hope this helps.