How do I update the credit card payment option from coming over automatically when syncing invoices from another program?

Hello flnice85,

Welcome to Community!  QuickBooks Online Payments is a great way to enable your customers to pay immediately upon receipt of their invoice.  However, please be advised that when you enable QuickBooks Payments or online payments, the options for credit cards is set by default.  At the moment, there isn't a way to disable it, so you'll need to uncheck the option as you process the invoice.

When using a third party app, I recommend checking the settings, to ensure a smooth transition when syncing your invoices to QuickBooks Online.  If you're not certain how to make the necessary adjustments, please contact the support team for your app.

If you have any other questions, feel free to reach back out.  We would be glad to help!