I'm not a SUN expert, but on AIX you just define /var/mqm/qmgrs/A and /var/mqm/qmgrs/B as different file systems.
It's also a good idea to have your logs in a different filesystem than the qmgr data. You can create filesystems for /var/mqm/log or just put your MQ logs in another, existing filesystem by modifying /var/mqm/qmgrs/A/qm.ini
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