Admittedly I don't full understand the instructions given in the plugin
Here you can select the thumbnail effect, NextGEN Gallery will integrate the required HTML code in the images. Please note that only the Thickbox effect will automatic added to your theme. With the placeholder %GALLERY_NAME% you can activate a navigation through the images (depend on the effect). Change the code line only , when you use a different thumbnail effect or you know what you do.
I've taken the code, and placed my gallery info inside of it:
rel="lightbox[nggallery id=1]"
And I've placed it on the page. It however does not work. Any suggestions? Thanks.