In the user management section for an affiliate user, on the Edit page, at the bottom, there is the "Affiliate Commissions Settings" field. Supposedly this is where one can specify a percentage commission to override the global and role-specific commission structures.

To test it, I created a product with a price of $100, and set the user-specific commission value to 10, thinking that means 10 percent. Unfortunately, in testing, for a purchase total of $100.00, the commission was only $0.10, not $10. Changing the user-specific commission value to 50, resulted in a commission of $0.50. So the commission value seems to be off by two decimal points.