OK, we received our first order and the email was sent out correctly except for the shipping method chosen by user.
So, to find out the method of shipment, I went into Manage Orders and clicked on the order and it doesn't show it in there either.
It simply gives me a selection box to choose method of shipping and to 'save' or 'Save & Mark as Shipped'. We only offer one method of shipping but it's important to know what the customer has paid for in terms of shipping and I'm not seeing it. It's also important for the email to included this information because that email is sent directly to the shipping department.