JBoss MQ and HornetQ are completely different messaging systems and are configured quite differently. You can't use JBoss MQ config with HornetQ.
Take a look at the user manual for an indepth guide for configuring HornetQ.
Also there are plenty of examples in the distro that show how to declare and configure queues.
Having installed HornetQ (as per quck start quide) on a vanilla JBoss 4.2.3GA there still appear to be remnants of JBossMQ (as per the default-with-hornetq/conf/standardjboss.xml mentioned above).
To rephrase one of my questions, are these JBossMQ remnants safe or do they need removing?
I'm not really an expert on JBoss application server configuration (which is what that is), but I'm pretty sure that is only relevant to JBoss MQ, not to HornetQ.