Amended return results in different payments on 1040x and 1040

I have to amend a prior return which has resulted in taxes owed.  The amended 1040 is showing a different amount owed from 1040X since the prior return had an overpayment applied to next year. Turbotax is subtracting the prior overpayment from the tax owed and adding an underpayment penalty on the 1040. How should I fix the 1040 (or not fix it)? Should I change the amount applied towards next year return on the 1040?