First you need to look at the Qtree security style for the exported volume/qtree. This will be either NTFS/Unix/Mixed.
If it is to only be used by Windows hosts, set it to NTFS, if this particular export is to be mounted on *nix hosts, and you want nix to handle all permissions, set it to Unix. Mixed should generally be avoided.
As for mapping users, this is done by modifying the /etc/usermap.cfg file on the filer. You can edit this in various ways, the easiest (but most unsafe) way to do this is by doing "wrfile /etc/usermap.cfg" from the NetApp command line. The perferred way would be to edit the file using a proper editor by mounting the internal "etc$" share via CIFS or NFS.
Documentation on the formatting of the usermap file can be found at the NetApp NOW Site which requires a login.
Here is a very small snippet of documentation which might get you moving:
#
# These are some sample "defensive" entries you may wish to use.
# They can be uncommented and placed as needed. See the System
# Administrator's Guide for a full description of this file.
#
# *\root => nobody # Map all NT users named "root" to have no
# # UNIX perms. They can still log in though.
#
# guest <= administrator # Map UNIX user "administrator" to NT guest.
# guest <= root # Map UNIX root user to guest. This should be
# # placed after any real "root" mappings.
#
# The next two mappings can be used to defeat the default mapping of
# the user names. That way only entries that are mapped previously in
# this file will be allowed.
#
# *\* => "" # Map all other NT requests to fail.
# "" <= * # Map all other UNIX requests to fail.
#
# The pound sign "#" is used as a comment character in map entries. The
# next three mappings show how to handle an NT user name which includes
# a pound sign. The name must be quoted. If the user account contains
# both domain and name, the username must be quoted separately.
#
# "#jdoe" => joed # Map NT user #jdoe to UNIX user joed.
# NTDOM\"#jdoe" <= joed # Map UNIX user joed to NT user NTDOM\#jdoe.
# "nt-domain\#jdoe" <= joed # BAD, won't work.
#
Basically, you willtake the name of your windows user, and map it to a valid unix user using something like:
domain\user => unixUser
You can also use wild cards.