It depends. Did your amendment make changes to the calculation of tax, or just to the application of the underpayment penalty after filling out the questionnaire in the Underpayment Penalty section? The penalty itself may not be a line item on the amended return, but you can account for it in the amount of original refund.
If you go back through the amendment process, it asks you to verify your original refund. You can change the amount of your refund on that line to show the refund that included the penalty. This will show that you get a refund of the amount of the penalty.
In your explanation for the amendment, state that you are amending to eliminate the penalty.
See this article and this one for more information on filing an amended return with TurboTax.