You can choose to set when an invoice becomes past due and add a late fee.
To do this go to settings -
Once on settings, click "Invoices & Estimates".
Toward the bottom of the screen Is the section "Invoice Settings"
To change how many days it is before an invoice becomes past due, change the number to the right of "Past Due Terms". In the example above it is set for invoices to become past due in 15 days/
To set a late fee after an invoice becomes past due, change the amount to the right of "Past Due Late Fee". In the example above, it is set to add a $5 late fee after 15 days.