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WSS2.0
In2.0, WSS will take all files that have the name "Webtemp*.xml" in 'Template\\1033\\xml' folder and aggregate them into one xml. each webtemp* file will point to a folder inside "Template\\1033\\xml" and will have the same name as the * in the "Webtemp*.xml".
So when you go and create a site, you'll be asked to choose a template and one of the templastes you'll see is the set of templates that are created in 'Template\\1033' in this case.
WSS3.0
In3.0, WSS will take all files that have the name "Webtemp*.xml" in 'Template\\1033\\xml' folder and aggregate them into one xml. each webtemp* file will point to a folder inside "Template\\SiteTemplates" and will have the same name as the * in the "Webtemp*.xml".
So when you go and create a site, you'll be asked to choose a template and one of the templastes you'll see is the set of templates that are created in 'Template\\SiteTemplates' in this case.