The colours are looked up through the hierarchy. First it is checked, if you set a colour directly on the component, then it fetches the colour from the lookAndFeel.
It is absolutely common to have multiple lookAndFeels, even of the same type. That way they can have different colour settings.
The LookAndFeels are also looked up from each parent until the root is hit.
I found the whole complex too cumbersome and wrote a system, where the component DOM inherits CSS like properties. Have a look at PluginGuiMagic or this thread:
