It changes colors in whole style using HSL color space.
If you have Photoshop, check out hue/saturation layer. Put it on top of all your layers, click "Master" selection box and select some color from list, change it. You'll notice that Photoshop will change that color and colors close to it in all layers.
That's exactly how this editor works. Even editor's default settings are adjusted to make it work exactly like hue/saturation layer in Photoshop. You select a color, change its hue component, editor changes that color in whole style: all css files and all images. Editor doesn't differentiate between different parts of forum, it changes all colors that match color you are changing.
I hope this helps.