When you integrate QuickBooks for Payment Processing, QuickBooks uses a default rate that is unique for each account and may match your Keyed Rate. To see your rates on your QuickBooks account, go here, scroll down to Payment Methods, and click "See rates".
If this rate is higher than you were expecting, you can request a rate reduction directly from QuickBooks. Here are instructions. You can find additional contact information for Intuit Payments Support here.