[Entity("EmployeeTable")]
    public class Employee
    {
       //Memebers of Employee
    }

[Entity("EmployeeType1View")]
public class EmployeeType1:Employee
{
//Memebers of EmployeeType1
}

[Entity("EmployeeType2View")]
public class EmployeeType2:Employee
{
//Memebers of EmployeeType2
}

var model = new FluentNHibernate.Automapping.AutoPersistenceModel();
// add assembly and the like to model
model.WriteMappingsTo(path);

forech(var baseclass in classesWithSubclasses)
{
    var doc = new XmlDocument();
    doc.Load(baseclass.getType().FullName + ".hbm.xml");
    // use xpath to separate the subclassmapping in its own file
}