Hi Thomas,
We would like to inform that -javaagent will be able to monitor any service as long as the Web service or any other activity is part of compile java classes so we request you to configure -javagent agent as referred in below on Tomcat server and define custom POJO rules if you do not see any BTs for Web service request.
By default we auto discovered Web servies requests as long it is supported framework as per docs, Hope that information helps
Refer docs:
https://docs.appdynamics.com/display/PRO39/Tomcat+as+a+Windows+Service+Configuration
https://docs.appdynamics.com/display/PRO40/Apache+Tomcat+Startup+Settings
https://docs.appdynamics.com/display/PRO41/POJO+Entry+Points