my answer is pretty simple, do not mess up presentation layer (Whole MVC application) with data access logic and data modeling.
Have at minimum 4 projects in your Visual Studio Solution, from bottom to the top:
1 - ProjectName.Interfaces (Class library, entities's interfaces);
2 - ProjectName.DAL (Class library, the only one allowed to even know the EF is used, the POCO entities implement the interfaces of project 1 using another file where you redeclare same objects using partial classes...);
3 - ProjectName.BL (Class library, Business logic, references the two projects above 1 and 2);
4 - ProjectName.Web (ASP.NET MVC application, Presentation Layer, references two projects 1 and 3 but NOT 2);
this to simplify things of course, based on my experience this is a solid design, a bit overkilling for very small projects but pays off in the long term.
in my view, the M of MVC, Model, is NOT the data model, is not the EF, is not there to do ORM bound to the specific database engine.
this answer is subjective of course and is based on my personal experience ;-)
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