There is a much simpler way of doing it that I have implemented on my multisite. It soesn't require any mods to theme files at all. See the thread here

All you have to do is upload the image you want with the media uploader and call it with the CSS mentioned in the other thread

Hello to all,
I found today a very easy solution, as the editing of the php files didn't work for me.

I just copied the wp_settings.php to wpmu_settings.php, as the script is just looking for that file.
Now it shows in different installations the supposed headers.
The header should be named atuahalpa_header_1.xxx and should be uploaded via the media upload of WP.
Easy and simple and works
BR Matzbach

Another thanks for the great details in this post

I can confirm that gmarsh's solution worked for me too - using Atahualpa 353 on WP3.0.1 multisite install.

Originally Posted by gmarsh

Thanks for this thread, it helped me out a lot.

I wanted to add that this did not work for me:

if ( defined('WP_ALLOW_MULTISITE') ) {

but this did:

if ( is_multisite() ) {

I just edited the three files and that was it. I was also able to upload the correctly named images using the wordpress Media Library and they were picked up correctly.