I noticed you had a live URL in the screenshot you provided so visited that site and had a quick look. The first thing I noticed is that the home.js file references elements in the HTML via the ID.
eg:
if($('#section5').hasClass('active')==true) {
This is not recommended when working with Kentico and for that matter any web forms app since the ID's are normally generated on the server to avoid conflicts. Instead you should look at using a specific class to target that element instead.
eg:
In the HTML code you the live site has:
<div class="section direstion-intor" id="section5">
You could modify this element to :
<div class="section directions-section direstion-intor">
Then in the home.js file you can replace "#section5" with ".directions-section"
Note: that the home.js file has lots of selectors based on ID and hence you would need to spend a fair amount of time figuring out the best way to structure these as classes. As this is mostly for animation, you should also look at how Kentico will be used for Content Management and hence how the links are being generated on the home page so you can structure the animations such that they are reusable and can be assigned to any section.