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.
You should be familiar with the remaining settings which will tell the service when to run and how often.
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
This will now appear as a charge on the applicable invoices.