IIS 6 on W2K3 lets you edit the metabase directly using a text editor like Notepad. To do this you enable direct metabase editing, but you need to know how to write well-formed XML since the IIS 6 metabase is written in XML, not binary code like in IIS 5.
If you make a change to the IIS 6 metabase however, say a configuration change to a website or virtual directory, that change may not show up immediately. The reason is because IIS 6 caches such metabase changes so it can write them as one chunk, usually within 5 minutes of when you made the changes. This is true whether you edit the metabase directly or use ADSI or WMI to do it programmatically using scripts.
So don't be surprised when you make changes to the metabase and they don't seem to "take". Just give it time. If you're impatient however, you can right-click on the IIS node in IIS Manager and select Save Configuration To Disk to have your changes applied immediately.