Go to Notifications on left menu. (If this does not display for you, please let us know)
From the drop down menu, choose each notification template and review it, and make changes to any part of it that you can edit. There are some parts that cannot be edited because they are based on dynamic content.
Note that there are different notifications for Orders, depending on whether they are shipped to orders or pickup orders. This way you can put in custom information that will appear only on orders that are for pickup.