Once you have the report in front of you, you can click the "Rpt" link to pull up an earnings report (like the one above) automatically for the chosen affiliate, or the "Hist" link to view previous payments that you've made to the affiliate. Once you're satisfied that the amounts due to your affiliates is correct (you may alter the amount due on the form to the actual amount that you wish to pay them, as well as leave a more customized comment), enter a "Paid Date" and press the pay button. This will mark each affiliate as having been paid the amount specified on the date entered. This will mark all clicks paid.
Should the amount due be less than the actual amount (ie, if you adjusted it), or if an affiliate was not on the report due to their not having earned enough during the time period, their clicks up to the time of the report are still marked as paid. The system will determine their carry over balance, and the next time you run the report, that balance will be added to any new earnings to determine the next amount due.
It's important to note that the system assumes that once you have run this report, you are going to follow up and physically pay your affiliates. Payments will not be made by the system directly to your affiliates simply by running the report.