If you use QuickBooks, GnuCash, or any other external billing or accounting software or service to process payments but also want to keep the Billing block within the EMR up-to-date, you can simply add charges and payments to patients' accounts in the EMR as usual. Payment method should be marked as "Other" or "Cash" when a payment or credit is added, and you may add notes to indicate that the payment occurred via your preferred billing service.
So, for example, if you have a charge to a patient's account and want to update the account to reflect the fact that the patient recently paid via your preferred billing service, you would open the Add Payment pop-up by clicking on the plus icon in the Billing Block of the patient's dashboard page and selecting "Add Payment/Credit." Then you would add a payment/credit to the patient's account in the desired amount, designate the payment method as "Cash" or "Other" (whichever your preferred approach) and add notes, if desired.
See also Help: Billing.