Using TurboTax you enter all estimated tax payments in the federal section of the program.  The payments flow to the correct tax return based on how you enter the payments.

To enter, edit or delete estimated taxes paid (Federal, State, Local) -

Click on Federal Taxes (Personal using Home and Business)
Click on Deductions and Credits
Click on I'll choose what I work on (if shown)
Scroll down to Estimates and Other Taxes Paid
On Estimates, click on the start or update button

Or enter estimates paid in the Search box located in the upper right of the online program screen. Click on Go to estimates paid

Or click on Tax Tools on the left side of the screen.
Click on Tools
Click on Topic Search
Type in estimated tax payments, click on GO