Hi - I haven't tried using multiple session factories, but it is fairly simple to work against multiple databases as long as these are on the same database server, in which case you don't need multiple session factories.
I don't know if your problem fits into that category, but here is some information:
1) Connect to the database with a connection string that gives access to all the databases that you require.
2) In the mapping document for your classes you set the "schema" property to the database that you want to use. For instance if class C1 is in database DB1 and class C2 is in DB2, set the schema to "DB1.dbo" for C1 and "DB2.dbo" for C2.
3) If you have a default schema, for most of your tables you can specify that in your NHibernate setup parameters, and then override the schema property of the classes that does not lie within the the default schema.
Check this resource for more information:
http://www.codeproject.com/useritems/NH ... x1915287xx
Hope this helps
Cheers,
Thomas