To set a custom commission for any of your affiliates navigate to:
Seller Dashboard > Manage Affiliate > Manage Active Affiliates > Your Affiliates.
By clicking the Edit button next to the affiliate you can change the default commission to a custom commission percentage. The number in the Payout field is the amount of commission the affiliate will receive for sales on that product. Custom Commissions are also applied to trials and 1st payments on recurring products.
If you have created custom commissions for any of your affiliates they won't be affected by a change you make in the product editor.