The Commission module must first be enabled.
Go to Settings, General, Modules, Commissions and set it to Enabled "Yes" then Save.
To set Commissions up in the Practitioner Profile go to Settings, Practitioners, Commission Tab.
Select the "New Rate" button.
You will get a popup to set the parameters for each commissionable Department, Category or Product & Service Item.
These commission rates take effect from the time they are set up. They are not retroactive.