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Hi Jodee and welcome to the RH community.
It sounds like all departments will use most of the manual plus their own specific section. As such you could have the main section (that all departments would have) as one project and (maybe) each departments as a separate project. What I can't say is how much of this departmental content is the same or similar between the different projects. If it is very different a separate departmental project sounds like the way to go. If it is very similar you could have all the departments in a single project and use build tags to filter out the departments you don't need.
I had the similar dilema recently whereby I have to print out of RH into Word to generate user documentation. The user documentation is considerably different than the structure of the online help.
I found it a nightmare to create one single TOC for printed and online. I created separate customised TOCs for both online and printed only which is far easier to manage and you do not have to set the topics to print only / online only etc etc.
Only problem i have is RH dies every 6 months or so whereby i get an egg timer constantly when i try and click any topic or function in RH. The fix to delete the CPD and XPJ files and then re-index the help to recover for me causes the 2nd TOC be be removed from the project which is not good. So my advice is to copy the project and before you apply the fix so you can re-import the TOC just in case RH does this for you too!!. There is nothing worse than creating a TOC from scratch especially if is rather large!