You can have your own J2EE web application sit alongside the Enunciate-generated Web service application. The only issue is that you have to "merge" the web.xml file that Enunciate generates with your own web.xml file. (Of course, you won't even have to do that with the J2EE 5 support for the webapp fragment.)
Fortunately, Enunciate provides a way to automatically merge your web.xml file into the Enunciate-generated one:
There are a number of examples/tutorials for integrating Enunciate with your favorite framework that may be helpful, too.