Windows Server 2003 does not have a Hyper-V role, so the Hyper-V counters don't apply to it. Windows Server 2003 can run Microsoft Virtual Server, but that is a bit different and I'm not aware of any counters for it. In any case, there is no problem with
running the Hyper-V template because the Hyper-V related counters in the template will be ignored because they don't match counters in the counter log.
The System Overview (default) threshold file should be all you need. Use it for the host and the guest computers as well. I treat guest VMs the same as any other Windows computers each needing their own counter log.
I spoke at Microsoft Tech Ed 2010 on Hyper-V Performance Tips. I'm sure the video of it is out there somewhere.
I'm glad the tool has helped. It has certainly helped me out a lot as well. :-)