If you are using IIS then you need to setup a specific virtual directory to the directory with your scripts in. You then need to map the .pl or .cgi extension to the perl interpreter as described in the docs. As you are in Win2000 you can do this via the application configuration button.
You'll have to then stop and start the server but that should do it. One caveat is that you will have to remove the shebang line from any scripts you write (the first line starting with #!).
HTH
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