Charging late fee's can be configured in your Clientexec installation by navigating to Settings - Plugins - Automation Services and configuring the Late Fee service.
Default late fee charge: You can choose to apply a standard late fee to all products that do not have a late fee defined. You can also leave this blank, and only apply late fees to certain product.
Day to charge late fee: This will charge a late fee X days after the invoice is due. You will need to enter a value here for the late fee service to run properly.
Next, you can set the late fee charge on a per-product basis. Navigate to Settings - Products - Products and choose a product you want to set a late fee for. You can define the late fee at the bottom of the pricing tab