I can help share some insights about processing invoice payments.
In Intuit, we have QuickBooks Payments that let you accept credit cards, debit cards, and ACH bank transfers for invoices you send and sales you make. It will sync with QuickBooks Online (QBO) automatically in which it'll categorize each processed payment on your chart of accounts. Then, once payment is processed, the money is put in the bank account you used when you signed up for QuickBooks Payments.
If you're still unable to sign up for QuickBooks Payments, here's what you'll need to do:
How do I process payments received in to my bank account from credit cards and atm payments so it appliesto the proper invoices?
What if the person that ran the credit card had issues (her computer just shut down) before the payment could record in quickbooks? The payment shows up in merchant services and our bank account but not in quickbooks.