You can give a one-time credit to an affiliate with a manual invoice. The next time your store payments, you will pay the affiliate the extra amount you set. Warning: after you make a manual invoice, you can not remove it. You must pay the affiliate.
Go to Resellers (Affiliate) Admin, find the affiliate, and click the Edit Reseller Admin Information icon. Enable the Manual Invoices check-box and click Save Changes.
Return to the main Affiliate Admin, find the affiliate again, and click the new Add Manual Invoice icon. Enter the amount to pay the affiliate and an optional note. Click Add Invoice or Add Invoice & Pay Now.