GoAffPro provides you with the option to mark affiliate payments as paid.
To mark affiliate payments as paid, go to the Pending Payments section in the Payouts tab of the GoAffPro admin panel.
Here, click on Mark Paid, after you have made the payment to the affiliate.
This will open up the Create Payment Note window.
Here, you have the option to add a Payment Note (which is for your reference) and a Partner Message (which is the message that will be sent to the affiliate with regards to the payment).
Finally, click on Create Payment.