I was able to figure out how to change the email auto message on a sales receipt.  It only took a few years for QB to change this in the system.  I assume you know how by now, but if not, here's how:

1.  Click Gear Icon

2.  Accounts and Settings

3.  Sales

4.  Messages - within messages, choose "sales receipts" from the drop down menu, edit your content and make sure you save it!