I use customer notes in the following manner - once a product has shipping I include a note stating that it was shipping using method X and will arrive in X number of days.
Edit mail/order_customer_complete.tpl and add the following where appropriate:
Code:
{if $order.notes}
Order Notes:
-------------
{$order.notes}
{/if}
Similarly, you can add this code to any other relevant email message.
As an admin, you should go to the order # and enter information into the "Order notes (not visible to customer):" area
I have no idea what the purpose of this area is but I have now given it new usefullness
No other templates need editing...