If you want to use another version of the jQuery library other than the default library used by the design mode in Kentico CMS, you would have to link it only on the live site, where the default jQuery library is not linked. You can achieve this by a simple context macro:
Visible property of a web part: { % PortalContext.ViewMode == "LiveSite" % }
Any text (e.g. head section of a master page):
{ % if (PortalContext.ViewMode=="LiveSite") { return "<script src='jQuery.js' type='text/javascript'>"; } % }