Permissions that determine whether or not a user can pay invoices, and what payment methods are allowed to do so, are set on the Pay Invoices tab of a profile.

This tab also controls the payment methods that are available to be used to checkout within e-commerce if this profile is assigned to an e-commerce page.

To find these Profile settings, navigate to Users > Profiles, select the profile of choice and click edit. Then select the Pay Invoices tab.