Why are estimated payments I made as self-employed not subtracted from my taxes?

If you've entered the payments in the correct spot(s), then the amounts should be coming directly off of the net tax due amount. Did you record them in the TurboTax system? By what you've stated it sounds as though you've paid them, but you might not have let the TurboTax system know that you paid them. 

Under "Federal" Tab, then "Deductions and Credits" section, scroll down a bit to the section titled "Estimates and Other Taxes Paid" and click on the "Start" button to the right (or, "Edit", if you've already visited this section). Make sure that you've entered all information and dates of payment correctly in order to receive the full benefit of the timely payments you've made. Then, go up to the top right of your screen and click on the "Forms" view icon. Search for your 1040-ES Form(s) and make sure everything looks right. You should be all set if you follow(ed) that path.