You need to configure directly to the queue manager and not through a VIP since the agent would be routed to specific queue managers.
With the MQ & Broker agent, within the MQMonitor.properties file there is a line
mq.monitor.list=
On this line you can add additional queue managers
mq.monitor.list=QM1@host1, QM2@host1, QM3@host2
Then you duplicate the base settings
QM1@host1.host=host.company.com
QM1@host1.port=5584
QM1@host1.delaytime=180
QM1@host1.monitor.manager=minimum
QM1@host1.monitor.queue=minimum
QM1@host1.monitor.channel=minimum
QM1@host1.monitor.channelinitiator=minimum
QM1@host1.monitor.pagesets=minimum
QM1@host1.monitor.log=minimum
QM1@host1.queue.filter.exclude.system=false
QM1@host11.filter.exclude.static=true
QM1@host1.filter.exclude.dynamic = false
QM2@host1.host=host.company.com
QM2@host1.port=5594
QM2@host1.delaytime=180
QM2@host1.monitor.manager=minimum
QM2@host1.monitor.queue=minimum
QM2@host1.monitor.channel=minimum
QM2@host1.monitor.channelinitiator=minimum
QM2@host1.monitor.pagesets=minimum
QM2@host1.monitor.log=minimum
QM2@host1.queue.filter.exclude.system=false
QM2@host11.filter.exclude.static=true
QM2@host1.filter.exclude.dynamic = false
Now if you have a large number of queues/metrics from one instance, you could copy the MQ agent to another directory and then have an agent per MQ Queue Manager.
Hope this helps,
Billy