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.
Payouts > Pending Payments
Here, click on Mark Paid, after you have made the payment to the affiliate.
Click on Mark Paid
This will open up the Create Payment Note window.
Create Payment Note
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).