for the case its still a valid question:
If you use Cifs shares with NTFS security-style qtree than group quotas is not an option. Only User or Qtree quotas are available. The only options is to use a 3th party tool like NTP QFS.
If you use Cifs shares with Unix security style (not likely) than group quotas are available. Unix group quotas can indeed be managed by the Netapp System Manager.
grtz,
Jacques