I have a question about the various email that can be sent and changing the content of that email.

I am changing the content of the email that is sent from my store to remove the ZenCart logo (sorry folks) and inserting my own for example. My question is, where do I save the changed email files? I've only seen one email directory and that's directly underneath the zencart directory. Assuming the override system works with email also, there must be a way of keeping the original files intact on the server. I do maintain all the original files locally as well as my modified files.