Got it. You can setup the Receipt by going to E-Commerce Setup > Receipts
http://screencast-o-matic.com/screenshots/u/1HxZ/1500484959992-73038.png this will send the Order Number
If you are sending the Invoice after purchase it does send the Order # even though it’s titled as Invoice#
E-Commerce > Settings and then click on Orders from the left side menu > Email Invoice upon successful payment
Examples
These currently are the only areas that the Order Id can be sent.