This same problem was a bit of a hassle when we first switched over to Linux. We were very used to the traditional Windows way of assigning permissions.
We basically overcame the problem by creating role based groups; ie. accounts group, management group, engineering group, etc. and assigning user accounts to the groups depending on their role in the company. With this said, you will also need to put in some thought as to the structure of the folders in your file server and change it if required. You would want to consider a wide-short trees instead of narrow-tall ones.
--== Anything can go wrong. It's just a matter of how far wrong it will go till people think its right. ==--