If you need to charge a late fee (or any additional fee) to an invoice, all you need to do is select the Add Items button on the invoice detail page. From there, you would just need to select "Fee" from the option listed on the drop down:
This will allow you to set up a fee with a GL Account Code if applicable and with a name, description and amount. Once the fee is saved, it will be on the invoice and you can process payment for this new, manual fee.
