I made a payment when I filed my extension that is more than my tax due, yet TurboTax is prompting me to make a payment with my return. How do I handle this?

When you requested your extension you were supposed to pay your estimated tax due.  Did you enter the payment you made into your tax return?  Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes 

Ahh yes, you're right of course. I didn't realize it was (unfortunately) already including the payment I made with my extension.

Thank you so much!