You can find the version and product level that you store is running by going to the backoffice (merchant interface) of you store and clicking on the ShopSite image at the top left of the navbar. In the footer between the 2 logos it will list the version, product type and storeid for your store. Note ShopSite would only be adding jquery if you have ShopSite 11 sp2 r2 or greater which is the latest version so if you have ShopSite 11 sp1 or 10sp2, 10sp1 etc you won't have any ShopSite Jquery.
Are you using any ShopSite template tags in your jquery code? If so you need to make sure you specify the PROCESS option in the include statement that is calling the jquery code or the template tags will not be evaluated.