You are a little confusing here.
What theme is the live site using ? Are you working out the upgrade from weaver II to weaver Xtreme using a cloned site?
If so, the cloned site is mostly allowing you to figure out the Xtreme settings and what other tweaks are necessary during the conversion, but overall, you would need to follow / redo the whole conversion process on the Live site after having practiced it on the cloned site.
This of course depends on what was involved in the conversion. The settings part you can download from the cloned site and then load them on the Live site after switching it to Xtreme, but the conversion of pages and shortcodes would have to be redone on the live site.
I assume you read
http://forum.weavertheme.com/discussion/11303/converting-a-weaver-ii-pro-or-aspen-site-to-weaver-xtreme
Once you have worked out all the settings on the cloned site, you will simply save the setting file and then, switch the live site to Extreme