other than shortcode

I am a newbie at this but I found this site
http://www.suwa.org/
and they are using your plugin. This is how I found out about NextGen. Now I would like to do the same thing as they have done in their site a fade in fade out image with thumbnails below on the home page and it is above all the blogs. I looked for documentation and I found how to use shortcode, but I need to put the code in my index file. I tried putting the shortcode in a post and it works, but how do I go about putting it in the index file below
<div id="content" role="main">
can you help me with this?
For now I have to work on my computer, this cannot go live as of yet

http://wordpress.org/extend/plugins/nextgen-gallery/