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You'll want to manually enter the transactions once you've already paid your taxes outside QuickBooks Self-Employed (QBSE).
Please check this article in case you want to enter them using the mobile app: Manually Add transactions.
On the other hand, connecting your bank accounts to QuickBooks automatically downloads the transactions. This lets you skip the manual entering and categorizing transactions: Connect Bank and Credit Card Accounts.
For more information about Estimated Taxes, here's an article for your reference: Pay Federal Estimated Quarterly Taxes.
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