The APM .Net Agent documentation provides the steps to configure a different profile for a particular application.
Basically the procedure consist in editing the web.config file of that particular application and adding the <configSections> and <com.wily.introscope.agent> sections from the <Agent_Home>\Sample.exe.config file.
There are situations though where only the agent's metrics are seen in Investigator and none of the application's.
The procedure is described at this section in the documentation:
All the .NET APM Agent versions
All the APM EM versions
All paths in the profile file are relative to its own location
However, If the new profile file is created in a folder other than the initial agent install path, then the directives will not be found and no metrics will be gathered for the application
For example, if the profile contains the following entry:
Then the agent will look for those files at the same path where the new profile file resides.
It is needed to
When a new profile is created at the same level than the default IntroscopeAgent.profile, WILY_HOME, then it will work just fine.