It's ok. =)
In any case, I think what maninacan really needs here is an explanation of the difference between the Window object and the Document object.
The Window object (accessed via the "window" or "self" variables) is the top level object. If you view objects and their properties as a tree, the Window object is at the very top, which stems down into many many other objects, like the Array, Date, Math, Object, and Document objects, and a bunch of other variables. Each of these stems down into more objects and variables. And functions, too.
The Window object, in general, represents the window (or frame) that is holding the web page that the script is being executed in. It contains things that are specific to ECMAScript and have nothing to actually do with the document itself: the Math object, for instance, contains mathematical functions. This isn't really related to HTML, but it's something a script might need. Same with the Array object. There are exceptions to this rule: the Location object (window.location) can be modified to change the location of the document. However, in general, the properties of the Window object have little to do with the document.
By the way: The Window object has two variables, "window" and "self", which refer to itself. That's why window.open() is the same as just open(). Both are the same as window.window.window.window.open(). It's a circular reference. All "global" variables are really just children of the Window object.
The Document object (window.document), however, contains things that are specific to the document being displayed in the window or frame. All the DOM (document object model) methods and properties of the entire document are contained within the Document object. The Document object is a huge branch of the tree. Inside it is every piece of data about every node in the entire document, including its style properties and much more. The most common way to get to these nodes is through document.getElementById('id').
The Document object also contains things like the document's location (document.location, which is separate from window.location, though they behave the same in some browsers, even when they shouldn't), the document's style sheets, and more.
So, when you want to change the appearance of the document, you must use the Document object. (document.write is the simplest way during page load.) To change the window (to open a new window or close the current one or other window-related activities), you use the Window object.
the open() method of the Window object (window.open()) returns a reference to the Window object of the new window that's been opened. In your first post, this would be mywindow. To access the document of that window, you can use mywindow.document.
Anyway, I think i've covered most of the important points, so I'll be off now.