First of all the majority of all the code was dumped in one class, this was the main library object, a web view, the method callbacks and so on. Obviously this all needed changing so I set about refactoring it all into smaller classes and thinking about how I can keep the majority of the Awesomium functionality away from the user.
At the moment I have:
This GUIActive/Inactive member was changed by adding a callback into the C++ from the Javascipt in the Webpage. I used the JQuery mouseover/mouseout methods to trigger these callbacks, this meant whenever the mouse hovered over one of my <div> elements in the webpage then the click's after this would only be sent to the Webpage and not to the Game Scene.
This seems like a fairly decent way for doing this at the moment, although there may come a time when I will want to have a User Input stack. As I currently only have the GUI and the Game scene that needs input I don't feel It would be beneficial to start engineering something more complex.
Plenty to do but I know as soon as I have all this Awesomium code seperated into it's own library I will feel loads better, there's nothing better than a good old tidy up :)