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I'll help you with your invoice payment concern, Hannah2.
When you receive a payment, you'll have to manually mark it as paid in QuickBooks.
Here's how:
Once done, it will be marked as Paid today.
If you have Payments set up, QuickBooks will automatically recognize the paid invoices once the payment is received. I'd suggest checking the payment status from your Merchant Services account.
Please let me know if you have more questions. I'll be right here to help. Have good day!