trade scripts + joomla or wordpress
 

Anyone running any trade scripts inside joomla or wordpess.

yes

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Do you just Iframe the scripts or is there any modules that add your toplist or galleries.

No, for WP you just put the tracking code in the index.php at the root of the domain or the root of where ever the main page is. Not on the actual template file index.php

Joomla it's been a long time so I can't remember how I tested it, but try the same thing.