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http://www.demacmedia.com/magento-commerce/customizing-magento-transactional-emails/

To customize a default Magento email template, simply navigate to the Transactional Emails page in your Magento backend via the path SYSTEM > TRANSACTIONAL EMAILS, then follow these 3 easy steps:

Click on ADD NEW TEMPLATE to create a new custom email template

Select the default transactional email template that you wish to customize from the TEMPLATE DROP-DOWN

Click LOAD TEMPLATE