Hi Branden,
I don't know anything about the 'Set CIFS share ACL', but I don't think you can set NTFS permissions from the Filer like you do for share permissions.
On NetApp Filer, The command 'cifs access' sets or modifies the share-level Access Control List only, not the folders/files beneath that share. The folder/file permsissions are set through the security tab in Windows Explorer.
Thanks,
-Ashwin
On the side note:
One way to see both permissions would be via Windows MMC (Computer->Manage->Connect to filer->Shared Folders->Properties). This should bring up both Share Permissions and Security tabs.