Did you try out your configuration yet? Which version of APM are you running? version of MQ?
The APM MQ Guide details things pretty well - definitely have a look.
As you indicated, deploy and configure both the MQAgent and MQMonitor .properties and add the MQ PBL reference to IntroscopeAgent.profile.
Looks like the handshake configuration is recommended to minimze overload. Also see the mqConfigurationSetup script (or manually make changes).
The mqheaderinsertion/read properties enable support in SOA dependency map. You can toggle the correlation identifier to use MQ/MQJMS message header vs SOAP or HTTP since some apps are sensitive to changes.
A change on the Enterprise Manager will also report Total Duration for Transaction Traces. Edit the IntroscopeEnterpriseManager.properties file located in the <Introscope Home>/config directory to add the following two lines:
introscope.workstation.transactiontracer.showTotalDuration=true
introscope.workstation.transactiontracer.showTotalDuration.sumAllTraceComponents=true
If you deployed the Management Module for MQ on the EM, the WebSphereMQ Cross Process Transaction Trace Health & Availability dashboard helps you check whether your WebSphere MQ infrastructure is properly configured for MQ Trace. The dashboard has traffic lights that show the status of SYSTEM.ADMIN.ACTIVITY.QUEUE, Agent-MQ Connection Status, Handshake status, Activity recording status, and Dead Letter Queue.
Hope that can point you in the right direction.