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Just my two cents: Running your own DNS does have a great number of advantages, it's not a great idea unless you have at least two servers dedicated to running DNS. Otherwise when one of your sites get's Slashdotted all of your domains are down, because their DNS is hosted on the same server as their sites.
Are you colocating this server, or is this in house? Either way you can talk to the people who provide you with IP space and see if they've got some DNS servers for you to take advantage of while you learn about DNS on a spare server.
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