The company I'm working for bought another company that's got its own domain. We've connected these together and noticed that both domains have got their own WDS server.
Let's call our primary WDS server WDS1, and the existing one of the domain of the bought company WDS2.
What I'm trying to do now is to boot into WDS1 from the other location. However, only WDS2 is recognized by the PXE boot options. So I'm guessing I have to change the DNS entry or something? Where do I start? I've noticed the old WDS server in the other domain's DNS. I'm not sure if PXE boot is DHCP related and not specifically DNS related?
Ultimately your PXE clients need to be told where to find WDS1 as WDS2 is still responding to their requests.
The PXE client will acquire an address from a DHCP server and then locate the PXE server, both of which are performed using UDP broadcasts. If the two servers are separated by a router (or on different segments) then the broadcasts won't be reaching WDS1, so I am assuming that your two WDS servers are on different network segments.
That I know of, there are two possibilities for configuring which server the clients use for deployment: using DHCP options and using IP helper addresses.
See the following article from the Microsoft KB which explains the difference between the two in quite some detail: http://support.microsoft.com/kb/926172
This one should also help you on your way: Managing Network Boot Programs (Microsoft TechNet)
Which option is better for you could probably be answered with a bit more detail about the network infrastructure that lies under your two organisations and their WDS servers, for example what address ranges are being used, routing mechanisms in place, how many DHCP servers and where they are placed, operating system versions, etc.