Sounds to me like you need to do some Sensor placement in order to track those methods and then set them to start PurePaths. You can enter the system profile -> sensors -> add sensor group (top right icon) -> browse the class cache and select the relevant methods. Once this is done, you can edit the method and check the box to allow them to start PurePaths (note, this option is only available at the method level).
You will then have to add the sensor group to one of your agent groups under sensor placement. Once you do hot sensor placement or restart the app server component the sensor should be placed and new PurePaths will be started when the method calls are detected.