Custom code in different versions of a template

Hi guys,
I'm using the great Purity III template.
I've copied the template several times, and each template has its own colouring. I want each section of my website have its own colouring.
Now I need extra css for each seperate color, so I've loaded an extra css-file 'blue.css' in the Blue template under the Custom Code tab.
But: this affect all copies of the template: when I open the Red, the Purple, the whatever template, I see 'blue.css' included.
Is this a bug?
How do I load extra files based on the active copy of my template?