Your feeling of having each department independent is most likely correct, Tina. You can run multiple Moodle instances on a single instance of Moodle software to accomplish what you want -- each dept will appear to have its own moodle but you will have a single software set to maintain. Search forums to get receipies how to do it. Should one department's usage take off, this setup will allow you to move them to their own machine with not much effort and nobody noticing it.