Bind/DNS with multiple domains, one IP
 

I have 2 registered domain names, which both point to my name server.
Originally, when i just had 1 domain name, it was the default one for my box, say domain-a.com

However, upon adding the second one, THAT one became the default, which I didn't want. So instead of my shell saying "user@domain-a.com" it says "user@domain-b.com."

Is there any settings anywhere in the conf file to change this?

Well if /etc/host.conf is set to
file, bind

Then it should be using what's in /etc/hosts. You can setup your primary domain in /etc/hosts and the information from named won't be queried.