Even though the task may seem daunting at this time, don’t worry, once you work everything out, it’s just a matter of implementation.
Basically, what I did was to break it all out on paper. I worked for a company with multiple offices worldwide so the first thing I did was break everything down by what office a user was in and then by what department they were in until everyone fit in to the appropriate place.
Another way to look at it would be from an HR point of view and just break down all of your users by what department they are in regardless of location, though, I did find it more organized to break them by location first and then department. It all depends on how you want the information broken out.
I hope this helps.