How to execute a function using this plugin.

Okay here I stand. I have installed and activated the plugin into my site and I need to execute the following function in it.

$(window).scroll(function() {
    $(this).scrollTop() > 0 ? $('body').css('background', '#f0f') : $('body').css('background', '#0f0');
}).scroll();

NB: The function is related to header image of my site

I tried to copy and paste the function in the plugin. But the plugin tends to show me errors which are not understood by me.

Do I need to define functions somewhere in my website *.php files?
If yes then where and how should I define it?

Please provide detailed answer.
Thanks in advance

http://wordpress.org/plugins/custom-javascript-editor/