It shouldn't be any problem. Just add the the AppDynamics system properties where you define JAVA_OPTS.
ie,
JAVA_OPTS="$JAVA_OPTS -javaagent:/u01/app/appdynamics/AppDynamics/ver4.2.2.0/javaagent.jar -Dappdynamics.agent.applicationName=$APPD_AGENT_APPLICATION_NAME -Dappdynamics.agent.tierName=$APPDYNAMICS_AGENT_TIER_NAME -Dappdynamics.agent.nodeName=$APPDYNAMICS_AGENT_NODE_NAME