Starting with the application agent for all application servers, you can go into that agent and remove any specific application server files or for that matter, add more as noted below.
There are a few base settings that you will need to deal with:
1. Multiple APM environments
We use a JVM parameter "-DagentManager=<mom>:5001" so we don't need multiple IntroscopeAgent.profile, one for each APM cluster.
2. Setting the agent profile
Each application server would have a different set of PDB/PBL files to include and those are set within the IntroscopeAgent.profile. You can set a different file using a JVM parameter "-DagentProfile=${AGENT_HOME}/core/config/IntroscopeAgent_websphere.profile"
Then copy the out of the box IntroscopeAgent, rename it for each application server, then within the profile configure the PBD/PBL that the specific agent host requires. If you have any custom PBD/PBL files, come up with a naming convention for the specific target environment.
So case, in the IntroscopeAgent.profile for websphere it would have the following:
introscope.autoprobe.directivesFile=websphere-typical.pbl,hotdeploy,webspheremq.pbl
but for WebLogic would be like
introscope.autoprobe.directivesFile=weblogic-typical.pbl,hotdeploy
So if you have two websphere environments that one has a skip.pbd while the other does not, you basically do the same thing and have a IntroscopeAgent_websphere.profile and a IntroscopeAgent_websphere_skip.profile. Then you set the one or the other in the JVM arguments to pick up the skip.pbd or not.
So, when you upgrade the application agent, I would highly suggest, starting your customization and settings from scratch. Don't just drop the pbd/pbl into a different version of the agent since there could be changes to the .profile or the pbd/pbl that will cause issues if you drop a different version. You should use your current pbd/pbl as reference and with that, always keep detailed notes on what you did and why you did it.
3. Placing the Agent files
Different application servers want/need the agent in a specific location, determine what works, document it, make sure that the configuration files and JVM arguments reflect that, and document it.
We have been using a variant of the above for quite a bit now and it has severed us rather well but cutting down on the number of agent install images we had to manage.
Hope this helps,
Billy