Forum Moderators: mack
/home/site1/htdocs
/home/site1/cgi-bin
/home/site1/logs
/home/site2/htdocs
/home/site2/cgi-bin
/home/site2/logs
Then set up Name-based Virtual Hosts [httpd.apache.org] for each site. Each user gets its own ssh/FTP access and individual password. (I assume you are setting things up on a Linux/FreeBSD or other Unix server.)
What I hate the most is nested sites, ie. placing document roots for supplementary sites within the document root of the primary site.