I am going to place my first physical server to a server room. I wish to use it also as an nameserver for my domains and I am missing some basic principle there. I can probably configure BIND etc, but how will the servers upper in the hierarchy learn that this is a nameserver for certain domains? To start with, I have several empty domains (they are not hosted and so far using nameservers of a big company).
I will be gratefull for any suggestions how to begin.
You will find a good explanation of DNS at http://cs.wikipedia.org/wiki/Domain_Name_System. In your case you basically need to assign your domains your server as name server. This is usually done in the control panel of your registrar or - in case yours doesnt offer one - manually by contacting your registrar.
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Although this isn't a biggie you'd have to make sure that all of your entries are in sync. Something that I've been using in the past to sync the DNS entries is through DirectAdmin. It has a special feature which allows you to add the admin of another server, it will then connect with the other server if there are any DNS additions or changes.
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You can make a career out of managing DNS, I know a lot of friends that I have helped do it. For most of the type of servers you will rent and run around here small DNS setups are easy to manage. Buy the Oreilly book on Bind if you really want to learn how to manage DNS servers.