Edit Email Templates in Magento

Default place/locale. You should not customize them in the filesystem.

app/locale/en_US/template/email/

Customize email and to create a new email template you have to go to 

admin -> system -> transactional emails -> add new template -> choose the base template from the drop down and edit as appropriate.

It is possible that your email templates are already saved into the database. Then you can assign the newly created template to proper functionality.

For e.g. if you have created new template for Invoice you can assign as follows.Go to

admin -> system -> configuration -> Sales Emails -> Invoice -> Invoice Email Template

And from the drop down select the template you created for invoice and save config.

Most important step.
- Clear the Cache.
- Go to System –> Cache Management
- Refreh Cache.
- If you have not enabled the Cache OR if it didn’t work even after refreshing the cache, then
- delete the cache folder present inside var (var/cache)