You get a duplicate location error if you try to add a software site that is already in your list, but is not visible. In this case you just have to activate the site in your site preferences.
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Open Available Software Sites Preferences
Click on "Available Software Sites"
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Activate the software site
Search for the software site you want to use (e.g. http://subclipse.tigris.org/update_1.6.x), set a check mark to enable it and click OK
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Select site
Select the update site from the Work with dropdown menu
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Done
Now you can use this software site normally and install the plug-ins you want.