Let me backup a second. Did you get the first refund from the original return? What did the email say exactly? Does it say payment completed? When you efile your tax return successfully and you choose to pay your fees from your Federal refund, the TurboTax program considers the fee paid, even though the federal refund has not been released yet. This is why you see "Payment Completed".
Or is the email saying they are going to charge your bank account? If the IRS is taking too long to send your refund and still holding your refund 36 days after your original estimated refund date they will ask you to pay the fees or they will debit your bank account. See, What happens if the IRS reduces my refund.
https://ttlc.intuit.com/community/payments/help/what-if-my-federal-refund-isn-t-enough-to-cover-my-t...
THEN if the IRS has not finished processing your original return and sent your refund you should not file the Amended return. You are suppose to wait for the first return to fully process and you get the first refund. There is no charge to amend a return unless you have to upgrade to a higher version.
