Stačí ve /www/ vytvořit soubor .htaccess a vložit do něj pravidla mod_rewrite:
RewriteEngine On
RewriteCond %{HTTPS} !=on
RewriteRule ^ https://%{HTTP_HOST}%{REQUEST_URI} [L,R=301]
# cele domeny (aliasy)
RewriteCond %{REQUEST_URI} !^domains/
RewriteCond %{REQUEST_URI} !^/domains/
RewriteCond %{HTTP_HOST} ^(www\.)?(.*)$
RewriteCond %{DOCUMENT_ROOT}/domains/%2 -d
RewriteRule (.*) domains/%2/$1 [DPI]
# subdomeny (s nebo bez www na zacatku)
RewriteCond %{REQUEST_URI} !^subdom/
RewriteCond %{REQUEST_URI} !^/subdom/
RewriteCond %{HTTP_HOST} ^(www\.)?(.*)\.([^\.]*)\.([^\.]*)$
RewriteCond %{DOCUMENT_ROOT}/subdom/%2 -d
RewriteRule (.*) subdom/%2/$1 [DPI]
# aliasy - spravne presmerovani pri chybejicim /
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^domains/[^/]+/(.+[^/])$ /$1/ [R]
# subdomeny - spravne presmerovani pri chybejicim /
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^subdom/[^/]+/(.+[^/])$ /$1/ [R]