1) You don't have to modify Apache settings for each site. Just create aliases for all the domains you want to use to be rewritten to ../index.php
The site access logic is controlled via ez publish .ini files. in /settings/siteaccess/site.ini find the section [SiteAccessSettings] and determine the mapping of domains/uris/ports to your logical sites.
2) If you want different content for your different sites, you should use one admin site for each and of course use separate databases.
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