You should wait until your E-Payment for your first return has been processed before filing your Amended Return. The two returns don't connect with each other; they are processed separately.
In your Amended return, you'll indicate that you paid the balance due on your first return. The 1040X should then show a Refund to you, if the amount owed to the IRS is less.
Here's more info on How to Amend a Tax Return.
@DPL1964
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