Hi!

Generally I'd advise to install ISPConfig 3 first, and then install Drupal since ISPConfig 3 takes over so much of the system. Though you should be able to make it work still.

You need to create a new site through the ISPConfig 3 interface. Once you do that, you then need to move your Drupal site to ISPConfig-managed site's web root. It will be something like:

/var/www/clients/client0/YOU_STES_NAME/web