Even thouh the jbosscache sar comes with some sample configurations such as mvcc-entity, nothing stops you from copy/pasting that file, producing a new one and adding your mvcc-entity-custom there. Once you have the file there, you can do several things:
1. Use a SharedJBossCacheRegionFactory as per docu and configure hibernate.cache.jbc.cfg.shared property with the location of the new configuration file.
2. Carry on using JndiMultiplexedJBossCacheRegionFactory, in which case you need to go to the CacheManager started by the server and made the modificatioins there.
If you want the cache to be deployed per application, you wanna be using option 1.
Again, this is all very clearly explained in http://www.jboss.org/file-access/default/members/jbossclustering/freezone/docs/hibernate-caching/3.5/en-US/html/configuration.html#sessionfactory-factories