enable-migrations -ContextProjectName MyProject.MVC -StartUpProjectName MyProject.MVC 
-ContextTypeName MyProject.MVC.MyContextFolder.MyContextName -ProjectName MyProject
This will add migrations to your MyProject project using the context in the MyProject.MVC. You need to make sure that the project with the Migrations has a reference to the project with your Context, i.e., MyProject references MyProject.MVC