Yes, you will need to enable this code immediately after enabling jQuery and before you enable Mootools.
<script>
var j$ = jQuery.noConflict();
</script>
Then you will want to find / replace all jQuery links $with j$, preferably using the automatic tool found in most code editors.
You also have another option - closing. It will look something like this if I remember correctly:
(function($) {
})(jQuery);
. $, jQuery, , , Mootools .