[Samba] samba/active directory permissions

[betty Snoop]

Using Debian 4.0.    I want to create one Share (eg.  Files) and have
subdirectories for each department.  This is so that users only have to
mount one share.  So it looks something like this:

Files
   -  Accounting
   - Human Resources
   - Enginnering
   - etc

Using Samba how can I give subdirectories different permissions using Active
Directory.   Would this be done by creating corresponding linux groups and
assign them to the directories at the linux level?   If so how do I map
Active Directory users/groups to their respective Linux users/groups.  I'm
trying to replace a Windows machine that is currently acting as a file
server.