Alan Gibson, one of our engineering gurus here in JDeveloperland, gave me this tip recently for developing both J2EE 1.3 and 1.4 services in the same application.
1. Add your base Java implementation to project1
2. Create project2 for your J2EE1.3 Web service
3. In the Dependencies tab of the Project Settings for project2, check project1 as a dependency
4. Publish your J2EE1.3 service in this project
5. Repeat steps 2-4 for a J2EE1.4 service
There is a bug in the J2EE1.3 service creation that means the node for the web service will show up in project1, but the crucial thing is that the J2EE1.3 web.xml file will go into project2, so this solution does work properly when you deploy or run it.
This is a good example of the way you can use project dependencies to separate your base logic from the service artifacts - even if you only have one kind of service implementation.