Suresh
Here is a link to two KnowledgeBases that explain in a little more detail about how to do this:
http://digital.ni.com/public.nsf/3efedde4322fef19862567740067f3cc/e503d0842606377a862569ea006ffd01?OpenDocument
http://digital.ni.com/public.nsf/websearch/12EF05DEA4FD8DCC862569E700750616?OpenDocument
As far as setting up Windows, once you have a bootable partition, you should be able to run the Windows 2000 setup. I would also try searching the internet for help on your specific error. Since the PXI controllers use a normal laptop hard drive, the rules and steps for creating partitions and installing OS's are the same
Regards,
Andrew Mierau
Applications Engineer
National Instruments