Wow. Something is going bad there.
If the installation is working correctly, dropping a module into the '/mod' directory (as a subdirectory of /mod), and visiting your admin page will automagically install the module for you. Then you can see it where you say you can't. Same with blocks (only in the '/blocks' directory).
If you haven't got too far yet, I'd suggest starting over. If you have, can you grant me access to your site for a look see? I might be able to tell you if something is out of place.
Incidently, love the subject of your course. Agent-based Simulation is something I was doing a lot of work with in the last few years.
mike