First you should have NEVER filed the amended return before the original return had been fully processed. Doing so can extend the processing time for the original return for months so don't send anything else and just wait for the IRS to sort things out.
Although the payment may have been debited from your account I can assure you the amended return has not been processed yet and will not be until the original return is out of processing.
Next review the 1040X carefully ... did you have the original refund listed on line 18 ?
Look at the form 1040X …
Column A should have the figures from the original return, Column C the corrected figures and Column B the differences between the other 2 which needs an explanation on page 2 of the form 1040X.
If you completed it correctly you will see an entry on either line 16 OR 18:
On line 16 should be the amount you paid with your original return. If you paid nothing already then this line should be zero.
On line 18 should be the amount of your original refund you received. If you have not received your refund yet then you need to wait for it. If the refund changes from what you expected then this line must reflect that change.
Then you will see your extra refund on line 22 OR the new balance due you need to pay on line 20.
