Funny you should ask this question. My last Windows certification tip was entitled Stick with Windows 2000 or switch to Windows Server 2003 certifications? and dealt with this very issue. Read it over, and if you have any follow up questions, feel free to post here or e-mail me directly.
The short version of that story, given your circumstances as described in your message, is this: Get the Win2000 credit(s) in the short run, then take the upgrade exam(s) in the slightly longer run to prepare yourself for Windows Server 2003. If history is any guide -- and it usually is -- most companies and organizations won't migrate to Win2k3 for at least another year or two. I hope that helps, and thanks for writing.
This was first published in October 2003