The quarterly payments were just estimates for the SE tax.  Did you send them in on a 1040ES?  Be sure to enter them.

You can type estimates paid in the search box at the top of your return and click Find and it will give you a link to Jump To it.

OR
To enter Federal or State Estimated Taxes Paid, including a state estimated payment made in January for the prior year, go to
Federal on left or at top
Deductions and Credits at top
Then scroll way down to Estimates and Other Taxes Paid
Estimated Taxes - click the Start or Update button

Yes it will calculate schedule SE.  
Self Employment tax (Scheduled SE) is automatically generated if a person has $400 or more of net profit from self-employment.  You pay 15.3% SE tax on 92.35% of your Net Profit greater than $400.  The 15.3% self employed SE Tax is to pay both the employer part and employee part of Social Security and Medicare.  So you get social security credit for it when you retire.  You do get to take off the 50% ER portion of the SE tax as an adjustment on 1040 Schedule 1 line 27.   The SE tax is already included in your tax due or reduced your refund.  It is on the 1040 Schedule 4 line 57.  The SE tax is in addition to your regular income tax on the net profit.

ok gotcha thanks for your response!

Just to clarify: it's great that your quarterly payments included an estimated amount for self employment tax.  On your tax return you will get full credit for those payments and will calculate the actual final amount and then reconcile the two.  So you might get back a bit of what you sent in your quarterly payments or might owe a bit more.

yea takes out all the guess work I suppose! the site that I used was painless1099 they help you handle your quarterly payments as a self-employed/independent contractor. thanks for your response!