If you have an application already deployed to WebSphere, there are multiple ways to go about updating the application. Probably the most common approach is to undeploy the current application and to then deploy the updated version of the application using one of these methods.
Another option is to create editions to roll out a new edition of an already deployed application.
If you only have a few files in the app that you want to update, such as a JSP page or a properties file, it may makes sense to do a partial update. In the WebSphere admin console, select Applications > Applications types > WebSphere enterprise applications > your app > Update. You will be presented with a few options.