Custom payment for affiliates

You can already validate the payment of the full amount of the affiliate commissions on the affiliate's user edition page, thanks to the small icon next to the total of the commissions.

There is no API to pay partial amounts of commissions. The way the system works is that each order has a commission, the id of the partner, and a paid flag which is set to 0 by default. So HikaShop displays the aggregate of all the not paid commissions of the partner.
When you pay the commissions via the interface of HikaShop, it switch the paid flag of all the orders of the partner.