At the first Moment i didnt understand whats your problem, but now i think i can help you...
The quick answer: Because you are new tu ezPublish it would be the easiest way to download the jquery extension here --> http://ez.no/developer/contribs/template_plugins/jquery_extension
Then go to the jquery Website and get the latest Version which is 1.2.6. replace the jquery.js with the Version you downloaded (in /design/standard/javascript)
Place your custom javascript to the same folder (only for testing, i recommend a custom extension for those things)
Go to settings folder of the jquery extension and open the file design.ini.append.php and include your custom.js script like:
[JavaScriptSettings]
JavaScriptList[]=jquery.js JavaScriptList[]=custom.js
clean the cache... your done and jquery with your custom javascript should run on ezpublish.
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