You can do this by adding this line of code to all your templates and email configuration, although you may not have much choice on whether it's at the bottom or top of the email.
<img src=http://YOUR URL HERE.png>
I added the code to the only area I noticed would take code, "Email Footer". It worked great, but obviously its not the real solution.
I need to find out where I should add the code to have the logo in the header.
Let me know if you have any other ideas.
The only way to do this would be to add that line of code into the original templates which are in the database and Web Help Desk folder.
I've not been successful in implementing this yet but if I figure it out I'll let you know.
For the time being, I think the Footer is the only viable way since if you upgrade, this won't be changed.
If you find the originals and alter them, an upgrade will change this back meaning you'll have to remember to do it all over again.