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You'll need to wait for the IRS to process your return, and you'll need to pay the full amount based on that return.
Once the IRS cashes your original check, or makes an electronic withdrawal of the amount you owed on your original return, you can file an amended return to include your estimated payment and receive a refund for that.
Please see the TurboTax FAQ "How to amend (change or correct) a return you already filed," below, for instruction on how to amend your previously-filed tax return.
https://ttlc.intuit.com/replies/3288565
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