You can set when an invoice becomes past due and add a late fee.
To do this, go to Settings (the gear icon on the top right).

Once on settings, click Invoices, Estimates & Receipts.

Toward the bottom of the screen is the section "Invoice Settings."

First, enter the number of days after the invoice is sent that you want the invoice to become past due and add a late fee to the invoice.

Next, choose whether you want the late fee to be an exact amount or percentage.
Note: Percentage is only available if you have auto-charge enabled. Enter the amount or percentage you want the late fee to be. If that is the only late fee rule you want, click the "save" button.
You can add more rules by clicking the "+ Add Late Fee Rule" button. Be sure to click the Save button when finished to save the new late fee rules.