samba 3 can't participate in an active directory domain yet. it can see it and read it, but not use it.
you have to make sure the workgroup in samba is the same as the domain name. then create linux users with identical names as their windoze names. then 'smbpasswd -a user' and set their password the same as their windoze passwords, after that you can create shares using the user name. There may be another way, but i'm sure it is involved....sql and fun stuff like that.