Yes, the starting point should be the amounts as changed by IRS.  Not sure this will fly with electronic filing but that doesn't speed processing, despite many who claim otherwise.  

When all else fails, read the Instructions. 

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.

https://www.irs.gov/pub/irs-pdf/i1040x.pdf