Lets consider default ASP.NET MVC application folder structure, so it\'s looks like this:
-App_data
-Content
-Controllers
HomeController.cs
-Models
Accou
I would put the EF-model (aka physical model) always in its own assembly or in a "core" assembly outside of main MVC application. The same applies for your business-logic / domain-logic / domain-services / etc. Separate the non-web stuff from the MVC-Web-Application.
This will help you re-use the core part of your app. For example when you need to expose it as a service, a command-line tool, migration-tool, etc.
Because storing this in its own assembly is so easy and takes you a few minutes I highly recommend doing this for each and every tiny app too.