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There are two ways to hide Auto-Pay: On the company or individual level. This setting hides the Auto-Pay option from the Customer Portal. In other words, Customers will not be able to opt-in or opt-out of Auto-Pay. An Admin User will then have to set up Auto-Pay for Customers.
To hide Auto-Pay for ALL Programs & Classes on the company level, head to the My Company page and scroll down to the Payment Settings heading.
Under that is "Auto-Pay Settings." Choose the one that says, "Hide Auto-Pay."
Individual Account Level
To hide Auto-Pay on an individual account, go to the Billing page of that account, and under Auto-Pay Settings, click the "Off" option: