Best Practive for setting up Application Folders

Is there a URL that Microsoft has for Best Practices or an accepted guide on setting up Application Folders on IIS? 

Our security folks are having us move all interactive scripting technologies (ascx, aspx, js, dll) to separate directories.  We are having to move our default home page which is a .aspx to a lower level from the root folder.

Any information would be appreciated.

Thanks

DJ