Found this little bit of code on the internet
Properties databaseAProperties = // get properties however you like
Properties databaseBProperties = // get properties however you like
SessionFactory databaseA
= new Configuration().configure("databaseA.cfg.xml")
.setProperties(databaseAProperties)
.buildSessionFactory();
SessionFactory databaseB
= new Configuration().configure("databaseB.cfg.xml")
.setProperties(databaseBProperties)
.buildSessionFactory();