On the clients, you can specify a search order that will be appended to names to make them fully qualified. For example, you could put mydomain.com and myotherdomain.com in the search order. When you go looking for the computer server1, it will append the first entry in the search order and see if it can find that, then the second, etc. The only problem with this is if you have two computers that start with (for example) server1 (i.e. server1.mydomain.com and server1.myotherdomain.com). It will find the one for the domain highest up in the search order unless you explicitly specify the fully qualified domain name. You can find this setting on the client: right click my network places, properties, right click network connection, properties, highlight tcp/ip, properties button, advanced button, DNS tab, append these dns suffixes button; enter your domains and put them in the order you wished them searched with the up and down arrow buttons. Also check the "use netbios over tcp/ip" setting seen in the WINS tab. If this is checked, you will be doing WINS resolution, not DNS resolution.
