For jQuery, if you are on version 8.1 (not sure if you are), you can disable the 'default jquery' for the site and use your own jQuery. V. 8.1 converted all CMS jQuery to $cmsj.
More on this at least is found here:
http://devnet.kentico.com/articles/using-a-custom-jquery-when-developing-pages-in-kentico
Note for 8.2, this is done by default, so you will need to include your own jquery regardless.