If you want to create a new theme for your instance, all you have to do is 
create a new folder in this /themes directory with the name of your theme, 
create a directory called "css" inside of it, copy the file /css/color.css
from the base directory into this new directory and modify the values in 
it.

you can also just copy of one of the theme folders in this directory
and modify the values to your liking.