Not WebSphere, but BEA WebLogic here. Our basic steps in the package are:
-Make sure the target instance is running, if not start it.
-Undeploy the current version of the application using script making weblogic CLI API calls. Version number is a %%PARAM%% passed to the script.
-File ADD to place the .war, .ear or .jar
-Deploy new version via CLI API script with version number passed as a %%PARAM%%
-Stop and restart WebLogic instance to force a write out and backup of the config.xml
That's the basics. There are a few more exact steps as well as the appropriate reverse order of steps for the custom Undo actions for each action in the package.
I hope that gives a good idea of where to begin even if it doesn't apply directly to WebSphere.
Do you also use BladeLogic to deploy the domain?