If you charge customers for being late, QuickBooks creates a separate invoice for the amount of the finance or late charge. When you sync, Bill.com gets the original invoice and the finance charge invoice. Both invoices appear on the website where customers log in to pay you.
If you're creating invoices directly in Bill.com, we recommend a similar approach. Simply create a second invoice for the finance or late charge to your customer. You can also edit your original invoice to show the additional amount.