Follow these instructions to do this - pay special attention to the part after the word ‘THEN’:
In Admin > System > transactional emails click Ã¢â¬ËAdd new templateÃ¢â¬â¢
Then under Ã¢â¬ËLoad default templateÃ¢â¬â¢ 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 Ã¢â¬ËLoad TemplateÃ¢â¬â¢
Under Ã¢â¬ËTemplate 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 Ã¢â¬Ësave templateÃ¢â¬â¢
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.