If I understand the question correctly, you've already got presentation and business layer based on PRISM architecture and you consider Entity Framework as data access layer.
The architecture
Julie Lerman has great course titled Entity Framework in the Enterprise available on Pluralsight. The course discusses best practices in terms of Entity Framework architecture in enterprise level applications which infers large sets of data.
EF lies in Data Layer, but Business Layer should depend on Repository/Unit of Work Layer. The essence of Repository Layer is to Encapsulate Redundant Data Access Code. The Repostitory consists of verbs like Get (GetCustomerById, GetAllCustomers), Add (AddCustomer), Remove (RemoveCustomer), Send (SendToDatabase).
The approach
Code first approach is the newest and I would recommend it. Comprehensive dissertation you can find on Code-first vs Model/Database-first topic on stackoverflow.
Domain Driven Design
Domain Driven Design (DDD) is a pattern that helps to manage large set of entities. It supports Separation of Concerns. Read more about it on dddcommunity. Watch the presentation Entity Framework in Core Business Applications and Domain-Driven Design Approaches that shows Entity Framework and DDD in practice.