For each table, you may add two more attributes named "entity" and "schema". entity is defined to prevent collision between entities with the same name in different schemas, and schema is your real database  namespace. Then you use the entity name in your HQL. We have tested this method with MySQL. On saturday, when I am back at work, I will be able to send you hbm.xml files if you need more details, but I think searching those two attributes will guide you to the answer.

As I know ,you need a sessionFactory for every one.
But If th DB is Oracle there is another way : you can let scheamas see each other.

Take al look at our configuration files attached to this email.
By the way, these are our hibernate  queries:

        List all = session.createQuery("from MBM.User").list();
        List all = session.createQuery("from IB.User").list();

One of my friends a solution mentioned at:
sandbox.sourcelabs.com/.../virtualization.html

It uses multi-datasource before getting hibernate  Session