Non-integrated Merchant Services
The integrated Merchant Services (Credit Card processing services) used in Checkout are provided by Forte Payment Systems (formally known as ACH Direct). If you want to use your own pre-existing Merchant Account with Checkout, you can, but it will not be integrated into the software.
After processing the credit/debit card payment through an independent Merchant Account, you can select Pay on the Invoice and select either Debit or Credit as the Payment method and then select Pay. The Invoice will be marked as Paid and the Payments and End of Day reports will reflect the correct total by payment method.