My 4/15/2016 estimated quarterly tax payment was taken out of my 2015 return. Do I enter it in as a payment I made or leave it blank?

Yes, you will need to enter it into TurboTax, there is a special place just for it.

To enter your 2015 refund that was applied to 2016 taxes in TurboTax please take the following steps:

1. Sign into TurboTax Online
2. Continue your return by clicking My TurboTax > Tax Timeline >Take me to my return
3. Click on the Federal Taxes tab (Personal depending on version)
4. Click on the Deductions & Credits sub-tab
   
5. Click on Show all tax breaks (if needed)
   
6. Scroll down to Estimates and other taxes paid and click Show More
7. Click Start/Revisit next to Other Income Taxes.
   
8. Say Yes on the very next page. 
9. Continue through the interview to enter your 2015 refund applied to 2016 taxes.