It sounds like a bad idea to both run ispconfig AND configure your websites manually.
Now I haven't used Ispconfig myself, but since it is to take care of everything I seriously doubt you can just deit a few config-files and actually get it to work.
If you absolutely want to configure manually then I suggest you completely separate ispconfig's conf and your own.
That means, for your websites, add a vhost-file - do not edit the files ispconfig uses.