So, to see if I get this right - when you add another virtual host, the static html goes in /usr/local/aolserver/servers/newvirtualhost, the dynamic content is in /var/lib/pgsql, and "packages" go in /web (/var/lib/aolserver - why didn't you go with /var/lib/openacs ?). Why are logs not in /usr/local/aolserver/servers/newvirtualhost/modules/nslog/*.log or are they, but symlinked across to /var/log/ ?
All of the static and dynamic data for an OpenACS installation is in /var/lib/aolserver/service0, where service0 is your service name, with the exception of the database's native files. The default install doesn't put anything at all in /usr/local/aolserver.