The email templates are a confusing part of Magento, but here’s what worked for me, and it doesn’t get changed everytime you do an update of the core code (like some solutions):
In Admin > System > transactional emails click ‘Add new template’
Then under ‘Load default template’ select the default template that you want to base your new template on from the dropdown. (This just saves you writing them from scratch).
Click ‘Load Template’
Under ‘Template Information, enter a new name (very important to id your new email from the default one!), then edit away to your hearts content changing whatever you want, and deleting the dummy phone and email address.
When you are happy, click ‘save template’
Repeat for as many as you want changed.
Go to System > Configuration > Sales > sales emails and change the selection by choosing your new email template names from the dropdown.
That should do it. And your emails won’t revert back to the default when you next upgrade Magento.