I have credit cards turned off as the default setting when invoices are generated. Is there a way to keep that default but override it for certain customers?

Good day, @mboothe.

Once you turn off the credit card payments for merchant services, this will automatically apply for all customers. 

Having the option to override this setting is unavailable in QuickBooks not unless to turn this on.

For now, you can turn off credit card payments by deselecting the credit card temporarily when creating the invoice transaction. All you have to do is to uncheck the box for Cards under Online payments in the Invoice page. 

Additionally, you can read the information from this article to learn more about QuickBooks Payments: Common questions about payments deposits in QuickBooks Online.

Feel free to click the Reply button below if you have any other questions. I'm always here to help. Keep safe!

@mboothe 

QB Payment doesn't provide such feature on the customer layer. You may find the feature on another payment processor and integrate it with your QBO.