Sorry, but the Extra Percentage fields in Seller Admin > View/Edit Affiliates can only grant a bonus percentage to a given affiliate. This bonus is calculated separately from any other commission calculations, taken as a percentage on the item total of every order that affiliate refers (including all items in the order, and regardless of whether the item would normally grant any commission otherwise).
If you want to grant some affiliates a 50% commission and others only 25%, the way to go about that would be to set your Common Share to 25%, then grant specific affiliates an Extra Percentage of 25% in your View/Edit Affiliates screen.
