Kpicx,
There isn't really any correct way of modeling as oppose to efficiency. Whatever tools you decide to use is a personnal opinion. For instance, many people say you should refrain from using the boolean tool. I say if you like using such and such tool, and the software has that tool, why should someone else tell you what tools you should and should not use. If the software includes that tool, it is there for a reason, and the boolean tool can come in handy at times.

Other than that, preparing your models to fit windows is not that difficult. However, it is kind of difficult to explain in words. Have you tried looking at some of the free videos that SimplyMaya offers? The cartoon dog video tutorial is a pretty decent tutorial. It does not get into how to cutout windows specifically, but it still shows you how to work effeciently. Also YouTube can be your best friend as well. Who knows, maybe you will find a video on how to cut out windows.