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.