I don't know if my understanding of what you want to do is correct but I would approach it like this.
Set up categories for each of your faculties.
Then set up courses for each of your main topic areas (or potentially group topics together). Your decision on this has to do with where you plan to go with it. If you only ever want to stick with assessments on Moodle then I would say group the assessments to keep things central and simple. If you plan to extend later and add course material as well as other collaborative activities (wiki's, forums, databases, etc) then I would say split them out so that later you can easily add material.
Then set up your quizzes. Create pools of questions so that they can easily be reused etc. Easiest way to do this is to get all your teachers to work on it. Set a target such as each teacher must contribute 3 questions. This will force them to get involved and create ownership.
After you've run a few classes through, go over the results and tweak questions (some will be too hard, others too easy etc).