One usually have one single and same PathPrefix for all siteaccesses using one content repository (DB + var directory). Some cases force to have administration interfaces showing all content beginning at the very top of the content tree (Node 2), in which case no PathPrefix is used.
I recommend going through this thorough tutorial : http://share.ez.no/learn/ez-publish/lots-of-websites-one-ez-publish-installation-adding-siteaccesses-in-ez-publish
Cheers,
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Nicolas Pastorino
Director Community - eZ
Member of the Community Project Board
