Copying JQuery Slider Problem – [SliderJS.com]

Hi Everyone! This is my first post to a WordPress forum.

I am working on implementing the JQuery slider from http://www.slidesjs.com/ into the Nature Fox theme.

I modified the CSS to my preferences and successfully linked my pictures into the slideshow. By itself, it worked beautifully in a web browser. I thought from there it would be simply copying the index.html code into the desired location within header.php. I did the copy and modified the sources links within the code to match up to proper images, css, and jquery coding. The only thing that shows on the front end is basic text.

http://www.bluephoenix-webdesign.com/test

Questions:
– I had understood that HTML coding would read within a .php file, is this right?
– Do I need to even copy in the code? Or could I link to it?

Link to Header.php coding — http://pastebin.com/bKFkRGXP

Any suggestions would be great!