Unfortunately I do not really understand your problem.
Is it about how "server" resolves to the exemplary IP-Adress or what?
The domains are handled as domains meaing there is a vhost for each domain you set. Thus you won't be able to access a domain via the "central" IP of the server with the domain name in the path to access it - if that is what you meant.
For this you could try to manually or half automatically (without changing the ispconfig code which would be ruined every update) setting aliases poiting to the real domain pathes, or trying mod_rewrite.
Nevertheless for me it makes no sense to configure domains and trying to access them like this.