All the HQL queries that jBPM uses are centralized in one configuration file. That resource file is referenced in the hibernate.cfg.xml configuration file like this:

<hibernate-configuration>
  ...
    <!-- hql queries and type defs -->
    <mapping resource="org/jbpm/db/hibernate.queries.hbm.xml" />
  ...
</hibernate-configuration>

To customize one or more of those queries, take a copy of the original file and put your customized version somewhere on the classpath. Then update the reference 'org/jbpm/db/hibernate.queries.hbm.xml' in the hibernate.cfg.xml to point to your customized version.