You install the application the same way you install any other application, however you have to configure the server to use Axis as the SOAP and Web Services engine rather than the default IBM Soap engine. This is easily done in the RAD (or WSAD) development environment, or through the Admin console on a running application server.
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: