Treat Partners As Internal Users
With Payment Center, your internal users have the capability to apply payments to an invoice using different methods. They can apply credit card, check, cash, etc. For your customers online, they are limited to credit card and eCheck/ACH, and so are your partners logging in through the partner portal.
With some businesses, however, they want their partners to be able to login through the portal and apply payments using all the different methods. To allow them to do that, go to Payment Center Settings and tick the box called Treat Partners As Internal Users.
For your partners to be able to do this, their Salesforce license should be of type “Partner“/”Power Partner”