I've not done this before it looks like the process may be to create a file called <b>contentstructuremenu.ini.append.php</b> in ezpublish/settings/siteaccess/site1. Put this in the file:
Replace "x" with the root node ID for site1. Then create a similar file for site2. Then clear the caches. Again, since I haven't done this I don't know if there would be any unintended results. For more information, see http://ez.no/doc/ez_publish/technical_manual/3_9/reference/configuration_files/contentstructuremenu_ini/treemenu/rootnodeid.
However, if you just want different sites for different languages only, then see "Using several public siteaccesses" at http://ez.no/doc/ez_publish/technical_manual/3_9/features/multi_language/configuring_the_site_languages.
