Hi Imran,
It is one agent per Tomcat JVM instance.
Once you have a wily directory setup for one Tomcat instance you can just copy it to a second Tomcat instance and the only change required should be to ensure a unique agent name per the link Hal provided above: Monitoring Apache Tomcat
Per that link if you want to avoid any agent profile file change, in the Tomcat startup script e.g. catalina.sh (.bat), you can add a third JVM property "-Dcom.wily.introscope.agent.agentName=..." as well as the usual "-javaagent:..." and "-DagentProfile=...".
By lengthy process if you are talking about the process to add the agent parameters to the relevant Tomcat startup script yes that does need to be done correctly but once you have it done once, again it should be a case of simply repeating:
Apache Tomcat - CA Application Performance Management - 10.7 - CA Technologies Documentation
If the catalina.* file is identical across the instances you can just keep copying the one you created for the first instance to the remaining instances.
Hope that helps.
Regards,
Lynn