Hello there, climbaccess-gmai.
I'd like to verify what application you're using in receiving customer payments so I can walk you through the steps on how to link it into QuickBooks Online. If the application you're using doesn't support the automatic application into your invoices, you can manually match the deposit in your bank feeds to the invoices recorded in QuickBooks. To know more, you click this page: Categorise and match online bank transactions in QuickBooks Online.
On the other hand, if you're using PayPal, when customers make a payment to the invoice, it is automatically created in QuickBooks Online and linked to the invoice.
Any other additional information is much appreciated. Take care and have a great day!
