Quarterly Estimated Self Employment Taxes paid via EFTPS

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 Jump to estimates paid

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

Federal estimated taxes paid are entered on Form 1040 Line 26

The Quarterly Estimated payments that you made for self-employment are reported as Federal estimated taxes paid and shown on Form 1040, Line 26 as DoninGA said above.

You paid the estimated payments for your self-employment but the payments aren't shown in a location solely for self-employment estimated taxes paid, just federal estimated taxes paid.

@theleeb