You can create two siteaccesses, each with a different index page--which can be under a top level node (2) in the node tree. This would be done with the sites sharing one database (and the same var directory). In this case, in each site access, edit site.ini.append.php:
[SiteSettings]
SiteName=Whatever
SiteURL=whatever.com
IndexPage=/content/view/full/388 # use the new root node for this siteaccess
DefaultPage=/content/view/full/388 # use the new root node for this siteaccess
RootNodeDepth=2
This will get you started. More needs to be done if you're using ezwebin, if you want searches and sitemaps to only show the respective sites, etc.
There's also this related post: http://ez.no/developer/forum/setup_design/valentin_s_multisite_guide_v_1_example_uses_ezp_v_3_9_4 .
You will likely want to look at the PathPrefix functionality in the docs as well, as it will enable you to skip a level on the URL for your sites so that they will appear to be at the root level. this setting goes in the site.ini.append.php for each siteaccess.