HDR shots: aligning photos

Hi.
I just read the 4 articles about HDR photography

( http://forums.dpreview.com/articles/9393651514/the-art-of-hdr-photography-part-3 )

and found them very interesting. But I'm just a beginner. So, although I learned that each software has its points of strength, I will try to choose one (probably Photomatix) and use just that, since it would be a waste for me to spend so much money for applications I don't even know how to use.

Here is my question: I read that among the software used for the article, Photoshop CS5 is the best for image alignment. There is even a link to download a customized script.

But what if I want to use Photomatix, and still don't want to rely on automatic alignment?
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I wish people could see the world the way I see it