By the sounds of it... you still need to use the folder paths when mapping drives, but with correct NTFS permissions, it doesn't matter because only the relevant people can go where they should.
Really, on parent folders, you want just a Traverse Folders/Execute Files (I believe that lets people access their subfolder but not present any folders if they browse)
Then once they reach their own folder, as you rightly updated, just their own permission... it's upto you whether you allow staff access to student areas...
If you go to the Advanced section of the Security tabs, you can use effective permissions to see what kind of permissions you would get as xyz user, handy for checking if it's correct.
As for en-masse (?) you can use CACLS, XCACLS or the VB variant (subinacl?) to change the permissions... but you'd want to set your parent folder permissions first, then loop through the rest individually.
NB: make sure you set Traverse permissions on "this folder".
NB2: That's the short of how it's setup here... although we split our staff and students away from eachother so they can't do anything regardless of correct/incorrect NTFS permissions.