The configuration of the ISPConfig system falls outside the scope of the "Perfect How-to's" for installing them.
Just register the 2 IP's at your registrar as being the "Authoritative" servers for "domain.com. (You can use hostnames, if your registrar supports glue records)
"A glue record is the IP address of a name server held at the domain name registry.
Glue records are required when you wish to set the name servers of a domain name to a hostname under the domain name itself."
When you've done that, all dns lookup requests for "*.domain.com" will be forwarded to one of those 2 IP's. From that point on, it's up to what you enter in de DNS admin part of the ISPConfig web interface.