How do I set up my own web application in addition to the default_app that is built into VAJ Websphere Runtime?

The answer is in the form of a document that is there on the IBM site which addresses the same. The URL for the document ishttp://www7.software.ibm.com/vad.nsf/Data/Document2202

Situations where this can be useful is when you are using IBM Websphere as the production environment and don't want to deploy your servlets/JSPs/HTMLs in the default_app under default application server.