First step is to include j query to your magento website.To achieve this just add a new line add js to your page.xml layout or you can include js in template/page/html/head.phtml .

After this just include jquery.noConfilct to remove conflict between prototype.js and jquery library
For this use following  snippet

var $j = jQuery.noConflict(); 

$j(document).ready(function(){
    //here you can add your jquery code and jquery

 $ is to be replaced with $j 

   as it is the new replaced variable 

for the jquery script
});