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Let me help share how you can enter payments from your customers in QuickBooks Desktop.
Normally, you'll have to create a receive payment transaction if you need to close out an existing invoice. Otherwise, enter a sales receipt if the payment if the sale happens within the day you receive the payment.
That said, here's a couple of articles you can read to learn more about recording a payment from your customers:
Since you receive the payment and deposit for the same transaction, consider creating a credit memo and decide how you wish to let your customer know about the overpayment.
Additionally, I've got you his helpful reference for a compilation of articles you can use while working with us: Sales and Customers for QuickBooks Desktop.
If you have any other questions, please let me know by leaving any comments below. I'll be here to lend a hand. Stay safe!