I often have projects with three of more models because we have many databases.
I would create a two EDMX set-up with two distinct contexts. Create your application DB1 Context as normal then create an additional context and only pull in those tables that you are interested in from DB2.
To make your life easier in the long run and easier to maintain generally just create a DLL for each model so that it has its own namespace and that way you can distinguish between users in DB1 and users in DB2 for instance and add or remove entities from one without affecting the other.
Each DLL would have an app.config connection string that gets yo to your data, such as
<add name="DB1Entities" connectionString="metadata=res://*/DB1Model.csdl|res://*/DB1Model.ssdl|res://*/DB1Model.msl;provider=System.Data.SqlClient;provider connection string="data source=(local);initial catalog=ClientDb;integrated security=True;MultipleActiveResultSets=True;App=EntityFramework"" providerName="System.Data.EntityClient" />
<add name="DB2Entities" connectionString="metadata=res://*/DB2Model.csdl|res://*/DB2Model.ssdl|res://*/DB2Model.msl;provider=System.Data.SqlClient;provider connection string="data source=(local);initial catalog=ClientMaster;integrated security=True;MultipleActiveResultSets=True;App=EntityFramework"" providerName="System.Data.EntityClient"/>
<add name="DefaultConnection" connectionString="Data Source=(local);Initial Catalog=Reports;Integrated Security=True;MultipleActiveResultSets=True" providerName="System.Data.SqlClient"/>
Just remember to copy each of the connection string from the Dll's App.config into your applications app.config or you web.config file for a site.
In your project reference the DLL's and then load your contexts.
DB1Entities DB1Context = new DB1Entities()
DB2Entities DB2Context = new DB2Entities()
You can now happily distinguish between DB1 and DB2 entities and use content from one in the other like this.
var address1 = DB1Context.Addresses.Single(a => a.AddressId == 1);
var address2 = DB2Context.Addresses.Single(a => a.Id == address1.GlobalAddressId);