Don't confuse the fees Intuit charges for processing cards of any type on your behalf. with the upcharge to your customer that your state allows you to impose.
Quickbooks does recognize PIN transactions at only 1% but only in QB POS (Point of Sale, software) https://quickbooks.intuit.com/payments/legal/TOC102017/standard-pricing-schedule-sep2017/ otherwise credit and debit cards have no difference of impact on your fees.
You would have to know ahead of time which of your customers is going to use a credit card rather than a debit card so that you could add the fee into the invoice before sending it to the customer