Vista - Security Templates and File System Security

I've noticed that a lot of our domain PCs have screwed up permissions
on the C:\ drive which are inhertited all the way down the file
structure. I thought I would use the security templates for Vista (i'm
running vista but there is a mix of vista and xp) in conjunction with
the Security Analysis and Configuration and Security Templates tools
fix the perms on my own PC.

On looking at the templates (which i downloaded from the MS site along
with the security guide) i noticed that none of them have any entries
under the File System node. I was expecting to see entries for the
root of the C:\ drive, the Windows directory etc such that I could
reset my permissions to the default Vista ones. Is this not where to
look to do this and if not how can I set my permissions back to the
default automatically?

Also, I know I can set permissions of the file system through group
policy but I'm guessing that setting the permissions for the root of
the C:\ drive (and have those permissions all inherited down the
entire file structure) is not a good idea?