If you have the correct user access, you can change the commission on each service line.
Go into the booking and select the service line, for which you want to change the Agency commission
Click on the box Manual commission and you'll see the commission field becoming available for change
Now you can overwrite your commission amount and system will recalculate the %
Note: If you would 'switch off' Manual commission, then system will revert back to the commission rules in Administration.