Presumably you're still using Media Center 11 rather than Media Jukebox?
The Media Center board is here
http://yabb.jriver.com/interact/index.php?board=3.0In answer to your question, yes you can change the colours.
When you download the skins they go into the MegaSkins Folder
for example:
"..Program Files\J River\Media Center 11\MegaSkins\Aruba"
Within each skin folder you will find a main.xml file
which specifys how the skin is laid out and in what colours.
Editing of this file is manual, there is no program to do it for you.
If you wish to change individual graphic files you can also do this
by taking one of the graphics files and editing them in an image editor.
More information can be found here:
http://wiki.jrmediacenter.com/index.php/MEGAMorphis