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Good morning, @marjorine,
I would be happy to help you! Since you're using QuickBooks Self-Employed, if you need to manually take a payment from a customer, you will process the payment through the Merchant Service Center. This article will walk you through the steps:
Process Payment in the Merchant Service Center
Since these transactions are not imported to QuickBooks Self-Employed, you will need to manually mark the invoice in QBSE as paid.
Hope that helps!