I'm not quite sure what u mean, what I want to do is tell ISPconfig that my httpd settings, vhosts, docroot, is in /opt/.....
ISPConfig requires that the services are installed in the default locations were the Linux distribution stores them. You can e.g. symlink the http binary, init script etc. The httpd config directory can not be symlinked, it has to be /etc/httpd or /etc/apache2, depending of your linux distribtion. so you can either symlink from opt to that directory so that apache finds it or you use mount --bind instead.
Personally I would avoid to compile apache manually at all as this leaves you also with the work of patching and updating it manually. Why did you compile apache manually instead of uing the one from the linux distribution? And if you have some very specific requieremets, why dont you compile your apache with the same settings as the one of the linux distribution?
If you like to use ispconfig, then I highly recommend to use one of the installation tutorials that you find here to install your server: http://www.ispconfig.org/page/en/documentation.html
