In order to use the base class as a foreing key / navigational property without primary key problems. You need to be using Table per Type or Table per Hierarchy.
In your case using that modelBuilder should do it.
protected override void OnModelCreating(DbModelBuilder modelBuilder)
{
base.OnModelCreating(modelBuilder);
modelBuilder.Entity<Employee>().HasRequired(e => e.PaymentType);
modelBuilder.Entity<Person >().ToTable("Persons");
modelBuilder.Entity<Employee>().ToTable("Employees");
modelBuilder.Entity<Company>().HasMany(c => c.Employees).WithRequired(e => e.Company).Map(t => t.MapKey("Company_Id"));
}
With this two table will be created. On names Persons will all fields for a person and one "Employees" for all fields for an employee. Both table will share the same primary key
You can get a really detailed explaination on Mortenza Manavi's blog