If you are a U.S. person, income reported on a 1099-NEC is taxable self-employment income to you regardless of where the organization is located, or where the work was performed. There's no special exemption just because the payer is an international organization, when the income is reported on a 1099-NEC.
Questions pertaining to estimated payments are usually asked later in the interview process. That may be why you are showing a penalty and balance due.
You can enter the payments manually under:
Federal → Deductions & Credits → Estimates and Other Taxes Paid → Federal Estimated Tax Payments.
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