I have:
By including prototype.js after jQuery, Prototype will override the value of the global $ variable. You just need to use:
var $j = jQuery.noConflict();
You can then use $j in place of $ in jQuery contexts and $ for prototype contexts. Here's the documentation: http://api.jquery.com/jQuery.noConflict/.
jQuery and Prototype both use the $ character so they will conflict.
If you wish to use them both together you will need to make use of jQuery's noConflict() method to release the $ alias back to Protoype
There is also a scrollTo jQuery plugin