The guide does not cover the Eclipse software update steps, but otherwise there is nothing different really between the stand-alone IDE and Eclipse with Wowza add-on, or between Wowza 3 and Wowza 4, as far as the basics of creating a Module, HTTPProvider, ServerListener or Wowza Project. They are the same wizards in the IDE, and the same steps to implement in configuration files.
In the Wowza 4 manager you can now add a Module to an application, and that is also not covered in the IDE Guide, but it is simple enough in the Modules tab of Application edit and follow the same essential step of naming the Module and adding the Class.
Richard