I think you may be referring to estimated personal income taxes paid in. You enter that in the Deductions and Credits section, the Estimates and Other Taxes Paid, then Estimates.
Self employment tax is entered on schedule SE as part of your Form 1040 personal income tax filing. The tax is added to your personal income tax and paid in through the Form 1040. As such, it cannot be prepaid, except with respect to its inclusion in estimated personal income taxes. Half of it is deductible on your personal tax return, and the deduction will be included in your tax liability on your Form 1040.
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