It depends where your dns is being hosted.
name servers records at your registrar tell the rest of the world which servers host your set of dns records.
If you're hosting your own dns records then yes. You need to set the name server records at the registrar to yourns1.yourdomain.com and yourns2.yourdomain.com
You then need to create the various dns records on your server. There is a very good wizard in ispconfig that will help you do this.
Think of it as a set of sign posts:
registrar > ns1 > your web server (or other service)
web server serves site up.