Each program has a default commission however you can over ride this at the product level when you add the product. The box that will appear will ask you to fill in the commission for this product if it different the programs default percentage.
If a program and product are already connected and you want to change the % you can do so by simply clicking the edit button to the right of the program name.
You can also override the commission for a specific affiliate. This is especially useful if you want to pay a star referrer a little more then the rest or reward a long time affiliate.
To do this you will find the affiliate within the program and edit their affiliate info.
Scroll down the commission box and input how much you'd like them to be paid