Just make the selection that you will pay by check...and then you just ignore the payment voucher.
The taxes due would still indicate the balance due at the time you e-filed...but the payment has been made (if you are sure you directed it towards your 2018 taxes due, and not as an estimated 2019 payment.
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Another thing people have sometimes done (but I can't guarantee it is proper) is to go the Deductions & Credits page, and then go into the Estimated taxes section, and include it as an "Additional Payments" in the quarterly Estimates section
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Unless you actually filed an extension with a payment..then it goes in with the extension payments in the "Other Income Taxes" section.