In most cases, use the ManagedResourceStore. It is meant to be used for application resources such as CSS, HTML, JavaScript, and images. It is good because it enables you to push your updated application in one step to the clients.
The ResourceStore is meant to be more of a specialized tool and should be used accordingly. For instance, if your application has user-generated content or user-specific data then it would be difficult to control it with a ManagedResourceStore. Using a ResourceStore to handle this dynamic content is ideal.