Amending a return after IRS reject

I filed my 2018 returns, and got a notice back from the IRS pertaining to missing forms.  Not sure why this happened because I had filed electronically with Turbo Tax.  I thought i had sent all the forms in response, but apparently they were still missing Schedule A.  As a result, they calculated my taxes based on the standard deduction.  I paid off the penalty letter to avoid any further interest or penalties.  Since then I received an amended document from my investment accounts, and the total of the overpayment from the standard deduction and the investment account change is over $700 per the amended return I've prepared.  But I don't know how to file this.  I started a new return as an amended return, but the 1040 that is printing does not indicate this.