Hi alisarmain,
Thanks for reaching out to us here. QuickBooks provides you with the tools and the resources that help you manage your transactions with ease. I'll be glad to share more info about using QuickBooks Online Payments.
While the function to automatically bill the fees separately isn't available, you have the option to manually calculate and add the fees to the invoice. Keep in mind that the fees will still be applied on the invoice total/payment. If you'd like to learn more about this, I recommend checking out the following resource that provides more info about: Intuit Payments Merchant Agreement. You're more than welcome to ask other questions as you go through the resource.
Let me know if this info helps. I'll be one message away in case you have additional questions. Otherwise, I wish you a great rest of the day.
