that is basically how it works. For like say lightbox pictures.. you just need rel="lightbox" in your image tag and if you wanted a popup type window to show html content. you just call the effect in a javascript link and pass the div you are looking to display. Really quite easy.. mess around with it a bit.. I am sure you will get it
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A number of people have already implemented Lightbox within Zenphoto themes, notably Chilifrei.
Another side too of Lightbox is just the plain old windowing as seen here in my implementation:
http://www.thinkdreams.com/zenphoto/demo/IMG_3502.JPG
(Click on EXIF Data).
I was looking at you source, what's going on there, you call the javascript and the everything wrapped by a certain div is displayed?
Thanks!