Just for consistency i would recommend you use the same implementation (AutoFac,Unity,Spring whaterver) of the container for all the conceptual areas.
If it's not hard to keep one container per conceptual area then do so. You will avoid problems when for the same dependency (ex IEmailService ) you need different implementations for difference conceptual areas (RemoteEmailService, LocalEmailService) . One disadvantage would be that if you have shared components you need to keep track of them and register them in each container for each area.
If your IOC implementation supports parent-child containers (AutoFac) you can have shared components in the parent container and component specific in each child container.
If your IOC implementation makes it hard to use separate containers for each area, don't fight it, either change it or use one global container but be careful when registering components.
Anyway make sure your code is IOC implementation agnostic. This way you can maybe start with a "one container for everything" and later if required move to "container per area".