I had fiddled with the presets. I guess what i'm asking then is, is it possible to change the - header, menu, footer presets colours of - dark, light etc, to different colours of my own choosing?
When we release upgrades template files will change and you will have to reapply all your changes again (that's if you can remember where they all are). If you keep your changes in a separate Custom CSS file you'll have no issues upgrading.