The webMathematica Server view can install webMathematica to your server. This is done with the Install button shown below.
When you click on the Install button the Workbench puts up a dialog that asks you for the location of the server and the location of the webMathematica zip archive.
When you click OK the Workbench checks to see if you already have webMathematica. If you do then it will confirm that you really want to delete it, and if you agree it will delete your old installation. The archive is then unpacked into your server.
This functionality is useful if you have made many changes to the setup of your server and you want to clean everything and return to an initial setup.
Note that the install works as a local filesystem operation. This means that the server must be on the same machine as the Workbench. For example, this might be a test server that is used for developing your web material.