Is there any way to safely change the directory where websites get set up after I've already installed ISPConfig? I want to make it /var/www/.
Within ISPConfig: Go to Management > Server > Settings. After that choose for the tab "Web" and change the field "Document root" within /var/www. On your server (as root) move all your webs (webX) with their symbolic links like www.mydomain.com to /var/www/. If you don't have the directory /var/www/ then you should create it first.