"Controllers" is MVC strictly correspond to views of your application and do what you want in your view. I think by "controllers" you mean the business logic for your entities. If you have created separate business classes for each entity, then that is the way to do it in entity framework. That is how it should be.
As controllers go, you can refer to any number of these business classes to achieve what you want, there are no technical restrictions.
For more information, visit this
CP article.