With the release of version 3.7.11 there is a new option in the 'Header Image' section of the theme options. This new option 'Header Images Directory' defines where your header images will be stored. It defaults to the themes 'images/header' folder.
You can point to a folder in your 'wp-content' folder by prefixing the folder name with some updirectory pointers. For example: say you add a folder to the 'wp-contents' folder called 'header-images'. to point to that folder you would enter '../../header-images' and you would now get your images from there.
The way it works is that each '../' moves you up a directory. you start in the 'atahualpa' folder so you are here:
Since this is outside of the theme folder, an update of the theme code will not tougch your images and since the path to the folder is a theme option, it will remain across updates.
MULTISITE since each multisite has it's own set of tables, each site can point to a diferent folder, so you could have
For Logo's and Favicons see the thread How to: save your LOGO/FAVICON images over an upgrades in the 'FAQ - Atahualpa' forum