If you have connected your NAS (SS4000-E) with AD already, assigning different permissions to your AD users (OU based) on the sub folders is described in the user guide that you can find from the[support site for SS4000-E|http://www.intel.com/support/motherboards/server/ss4000-e/], nonetheless I have attached a copy of it that you can find with this post.
Read through page 48 onwards.
Page 56 is perhaps what you are looking for but do not forget to read the Notes and Precautionary measures lest you end up losing data.
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