Then we need to know, where ISPConfig grabs the files needed to create a new site. That is, the web folder, ssl, backup, etc..
It is all created by the apache plugin. Take a lookat /usr/local/ispconfig/server/plugins-enabled/
Like webguyz mentioned, it is very likely that your setup will not work cleanly later and it is unlikely that you will be able to install any ispconfig updates on your server as your structure is incompatible with ispconfig.