You should put it in the template used to view the node.
ie: if you want to remove the right panel when viewing a folder object, you will put it in the "full/folder.tpl" that you will override or that is already overriden in your config (http://ez.no/doc/ez_publish/technical_manual/4_0/templates/the_template_override_system)
Cheers, Hakim
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