for most domains you need multiple dns servers. you can run a "normal" dns server on your server parallel to all the other services.
Even if you setup your domains with just your one dns server or trick the registrar by using multiple ips for your server it would be not failsafe. When your dns server crashes all domains will be unavailable.
The rackspace DNS service is free and is redundant on a global scale.
A con is that you are not able to control the Raackspace DNS Service through ISPConfig and its API. Unless you program a module using the APIs of the service.
To answer your question about what nameservers to put in on domain registration:
You must provide the nameservers/IPs handling the entries for the domain. If you use the rackspace service -> hostnames/IPs of their servers. If you use your own DNS server -> hostname/IP of your server on which the dns server is running.
If you use your own server(s) as nameservers I would highly recommend to use the Rackspace DNS service for the domain providing the subdomains for the nameservers. Example: ns1.your-domain.com, ns2.your-domain.com ...
Add these A-Records to the your-domain.com Zone on the Rackspace DNS Service. Otherwise your Nameserver is resolving its own Hostname which is not best practice for good availability.
Although it might be written a little bit complex I hope I could be of some help.