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No. It will not update your balance on TurboTax. If you have not already filed, when the program asks for payment, you can just tell it you are going to send a paper check. This will let the program know you have paid (and then you are free to pay however you wish). Regardless, TurboTax will always show a balance when you log on or look at the refund meter. This has no effect on your payment with the IRS whatsoever. If you made your payment, then your balance is cleared.
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