If the IRS accepts your return, then you have to wait until it has been fully processed and you have received your refund. THEN you can prepare an amended tax return 1040X and mail it in. You cannot e-file an amended return. Meanwhile, DO NOT change anything on your return until you start the amended return.
Ok ... from the 1040X instructions on Column A ... notice the words "it was changed by the IRS" ... you don't know if the IRS will change anything until the original return is fully processed .... if you send in a 1040X before the IRS has finished processing the original return then you could make the problem much worse and it could take months to resolve the issue ... in the years I have been doing taxes and the 50+ years my partners have done taxes we have had to clean up big messes from just this sort of issue ... so do yourself a big favor and wait for the original return to be fully processed and the original refund is in hand before you amend anything.
"Column A. Enter the amounts from your original return. However, if you previously amended that return or it was changed by the IRS , enter the adjusted amounts."