The AutoWindows collection returned by the Application object contains all the windows in the application, including the plot window, the worksheet window, and the template window.
The AutoWindows collection returned by the Document object contains all the windows opened on the parent plot document.
The AutoWindows collection returned by the Worksheet object contains all the windows opened on the parent worksheet document.
This example shows how to reference the plot window.
'Declares GrapherApp as an object
Dim GrapherApp As Object
'Creates an instance of the Grapher Application object
'and assigns it to the variable named "GrapherApp"
Set GrapherApp = CreateObject("Grapher.Application")
'Make Grapher visible
GrapherApp.Visible = True
'Declare Docs as Object
Dim Docs As Object
'Assigns the Documents collection to
'the variable named "Docs"
Set Docs = GrapherApp.Documents
'Declare Plot as Object
Dim Plot As Object
'Creates a new plot window and assigns it
'to the variable named "Plot"
Set Plot = Docs.Add(grfPlotDoc)