Payment information to the affiliate can be viewed from the 'Payments' link from the customer record in the customer listing. This will show the affiliate's total commission earned, and the value of any payments made to them.

Any commissions earned that have not been paid yet will be listed. If you pay a commission (or issue a coupon for it instead, if your terms are to pay commissions as discount coupons instead of as cash), you can check the box next to the commissions paid and click the 'Set as Paid' button. A payment for the total amount will appear below, while the commission records will disappear. If you make a mistake, or cancel a coupon/payment, just select 'Mark as Unpaid', and the commissions will be unpaid again.