you are right on the money as far as I can see.
I have configured tomcat and JBOss 2.4.4 separately without a problem however it took me 5 weeks to set it up and unless you are really really patient OR just won't let it go (like me) you are in for a real treat.
the only way to scale is have them separate. how can a web server and an application server run on the same box and be scalable?
I am no expert but for me separate boxes is the only way.
If you need questions or examples I have done them. It was awful but now that I am done I am happy.