There is a hierarchy to those email templates.  In the EDMM screen, click on the flashlight (not the magnifying glass) to see what templates are set up.  A template for a specific Module and/or Document Type will override the one you have showing now for "All" modules and document types.  The system will use the most specific template.  I always made a point to set up a separate template for each Module code at the very least, and often for each Document type as well.  For example, if I am sending emails for Sales Order Confirmations and Invoices, I would have a different template for each of those Document types.

Hollie