I came here because I was having issues with implementing a jQuery script into my design and the answer provided was not enough for me to find my error so after a pain staking process I found the answer and here it is:
In order to properly use a jQuery plug in, it is NOT necessary to include the jQuery library in the head. Webflow already loads it and it does so before the end of the body tag
So first load the plugin by pasting its location before the end of the body tag in your site´s “Custom Code” settings. Should be something like this:
<script src="http://pathtoyourscript/thescript.min.js"></script>
then you can load the functions like this:
<script>
$("button").click(function(){
$("#div1").fadeIn();
});
</script>
Hope it helps 