DNS server configuration

I am setting up DNS, Wins, DHCP servers.
DHCP, WINS even the DNS server seems to be working properly. We are not connected to the Internet directly, I have a MS Proxy server for that purpose. But are connecting some of our computers to another company’s hp3000, their IP address is different, we have a router setup. It seems that our computers take a little longer to connect to everything, EMail, specially to the HP3000 since its in a different subnet. I created Host file and its make it a little better, but I wonder if the DNS is working at all.
Q: do I have to create and entry for the router?, How do I tell the DNS about the other subnet?.