Well, building your own missions is possible, but the tools which are required to do that are not included. Building missions is something for developers and it aint easy. But if you are willing to learn, there is a website with a lot information on that subject:
https://fsxmission.com/live/modules.php? ... ningCenter
The multiplayer mode is for people who want to expiriment the realism of real ATC communications or just fly with other people together. It is possible to be the tower and set the frequenties, give directions to other aircraft (other people connected) and you can choose to connect a headphone/microphone to be able to talk.
You can also share an aircraft with one other player (be the co-pilot for example). You can either join or start a session. Your session will be visible in the session list in gamespy, so other people can join your session (you are the server in that case). In ATC mode, you are in the tower of the airport of your choice and you can look out the windows of the tower in the virtual cockpit mode, just like controllers do in the real world. There are various control panels in the 2d cockpit mode, including a radar screen which is close to a real ATC radar screen.
Unfortunally, not everyone is playing along in a session. You can set some restriction before you start the session, but as a host, you can not delete or ban people. And if you leave the session (your own session), everyone connected will be disconnected. Of course, if you join a session, you can leave and join at any time and it will have no effect on others.