I have the following project structure:
/Views/Shared/_Layout;
/Areas/Area1/Views/ControllerName/Index;
...
You specify a layout using:
@{ Layout = "_Layout"; }
If you want to make this easier to change all at once. Perhaps you could just set it as a view bag variable and pass it in on the controller. To make it even easier you could create a base controller that the other controllers inherit from and have it assign the layout to the view bag there.
Not sure why routing would need to change or perhaps I am not understanding. Hope this helps :)