The server running WebSphere_Portal needs to be started before you begin the update process.
Load up your web browser and login to the WebSphere Application Server. This is a seperate service running on your webserver. The port for this will vary based on your server and WebSphere Portal version. In a standard installation the urls for the console will be:
WebSphere Application Server 6.1 _https://\[server\]:9043/ibm/console_
WebSphere Application Server 7.0 _https://\[server\]:9043/ibm/console_
After logging in to the console, you will be able to install the application following the process below.