Hello, HoncoopGold19.
I'm more than glad to share what I know when processing credit card payments in QuickBooks Online.
Are you referring to your online invoices' payment method check boxes? If so, the system will automatically process the payment whenever your customers pay their dues. Did you happen to disable the Online payment methods in your invoices? Unchecking the box will just record the payment manually (no processing will happen).
However if you enable the Process payment box, this will be processed by our Merchant Services system.
If you're referring to your sales receipt, then the same can be said whenever you check or uncheck the Process payment box. The payment will be processed whenever you check it. Otherwise, the transaction will be marked as paid manually (live payments aren't processed) regardless if the credit card details are saved or not.
This article can tell you more about processing payments in QuickBooks Online.
Did you encounter any problems while doing your tasks in QuickBooks Online or your Merchant services account? Our articles can definitely help you out. They're packed with information and guides for a certain process in our programs. Take a look at them here. You can change the product (QuickBooks Online or QuickBooks Payments) by choosing one in the Topics for section.
Do let me know if you have other questions with QuickBooks Online or your Merchant Services account. I'm more than happy to offer help again.