In Setup > Email Templates there is a single section called Common Template.  This allows you to edit the basic information like address and to add text to be inserted before or after each type of email.

The xslt code for each email template is stored  in /www/_spire/master/modules/ecommerce/emails   These files are part of the software and can not be edited in this location.  If there is a change or a bug it should be fixed in the software.

If there is a need to customize the layout or functionality of an email template on a per client basis, you would need to copy the specific file from the module folder /www/_spire/master/modules/ecommerce/emails to the client folder /www/WEBSITE/_sitedata/data/ecs/emails

Once the file exists in the client folder a new section will appear in the administration where you can edit he content of this template.

The current files that can be customized are 

order_html.xsl
delivery_html.xsl
invoice_html.xsl
package_slip_html.xsl
estimate_html.xsl
giftcert_html.xsl
recurring_html.xsl
recurring_success_html.xsl
recurring_error_html.xsl
recurring_expiration_html.xsl