If you would like to add a late payment/interest/finance charge to an invoice you can do one of 2 things:
Create a new Slip for the additional charges on the client's project. In the comments of the slip, you can put the reference to the original invoice number and the reason for the charge. Invoice that charge separately and send it along with a statement to the customer so they can see their statement as well as the new finance charge invoice for more details.
Delete and restore the slips of the original invoice. Go to Billings Pro > Preferences > Numbering to reset the invoice numbering to the original invoice number. Add a quantity slip for the amount you’d like to charge (You can create a category for interest/late fees to track in reporting). Recreate the invoice with the original date and due date and resend it. You can also generate a statement which will reflect the new account totals.