The company I work for has a dedicated server with Windows 2003 installed. We primarily use it as a web server and file storage system for our virtual employees.

When I was registering a new domain name at Register.com, I realized that the majority of the domain names we own are not pointed at out DNS server, but instead use the register.com DNS servers. The IP addresses at register.com are then set to our server's IP address.

My question is what would be the best practice?

I can setup a DNS server for the box and then tell all other domains at register.com to use it. Or, I can keep the configuration the same and just tell register.com which IPs to use. As it is right now, it just seems unorganized.

if it aint broke dont fix it , man

OK, I can agree with that, but when adding a new domain, would you set it up to use our server's DNS server, or use register.com's DNS server?

I would point each name directly to your DNS server. Going through register.com's DNS server adds another point of failure.

That's a good point Eric. I hadn't really thought of that. I was thinking that if our server's IP address ever needed to be changed, then I'd have to go back to register.com and manually change the IP address of the 60+ domain names we own.

Do you know if there is a performance hit (on our server) if the 60+ domain names were set to our DNS server (which is on the same physical server that runs our websites, email server, etc)?

I would expect technically there to be a performance hit, since your server is doing more work. In the real world,you probably wouldn't notice depending on your hardware and the current workload.

how much trafffic do you get?