If I understand correctly and if you have a working war file which runs even outside WAS, you don't need to change anything in WebSphere, just deploy the war (perhaps using the Admin Console) and access the Web Services. axis.jar and other relavant jars should be there inside your WEB-INF/lib, that's all.
Check the list of available service using following url:
http://<your> server>:9080/<your context>/services
Does it make sense or I am totally out of context
Rudra Pratap