If you want to override application styles etc. Edit this file if you want to override standard CSS styling

design/customtheme/css/override.css

Edit this file if you want to override widget styles

design/customtheme/css/widget_override.css

I also suggest to have a look at http://livehelperchat.com/how-to-make-unbranded-version-of-live-helper-chat-223a.html this article. There is prepared extension for all things you may need to customise the app.