You can make the payment before you file the amended return, just be sure when you make the payment that it is designated as being for the correct year and tax form so that it will eventually match up with the amended return once processed.
On the off-chance that after your tax return is processed and you then receive a bill, call the IRS and provide them with the reference number from the receipt for your payment so that they can match the two items together.
@missy11
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