Hello Craig23
Currently the pay now to receive payments through the invoice and the pay now button is only for the third party integration with Paypal.
There is an alternative direct payment but not through the pay now on the invoice.You can set up direct debit mandates through QuickBooks Online and when you send an invoice with the accepted mandate on it would then on the due date start the process of applying for that payment at the bank and then close the invoice in QB as paid.
Emma