If you have taken the wrong payment details, issued a refund or for some reason don't want to show a payment on the invoice you certainly can!

Please go into the order and click on the Checkout tab on the workflow bar. Scroll down to the bottom and click on the Payment History tile.

All you have to do is click on the check box to have to display or not display on the invoice (filled in with blue means it will display).

As long as you have Received Payment component turned on, on your invoice template, you will see the payments that are checked off show on your invoice.