Go to Module manager open module by bodule and whereerver you see "Load JQuery" (this name can differ form case to case ) property disable it.
Then also go to plugin manager and do that also.
Then open index.php of template and check if there is already reference there. If yes you can just modify it to reference new files you downloaded or delete it and put above 3 reference lines in that order as much close to begining of <head> section as it can be.
To chack you have one and only exactly one reference use "View source" option of your browser when you go to your site. js. References can sometimes be in place where module is rendered so you need to check all source. Easiest way is to text-serach "jquery" in page's source.