Go the second route.
wwwroot is simply there as the container for the default website for the server. If you delete the default website from within IIS, then you can safely remove this directory. Regardless, your sites have nothing to do with the default, so they should be in their own folders under inetpub.
That said, we sometimes have multiple “types” of sites on the same server. For example DEV and QA. In this case I would structure it as:
c:\inetpub\dev\site1
c:\inetpub\dev\site2
c:\inetpub\qa\site1
c:\inetpub\qa\site2