All you need to know can be found here: http://wiki.flightgear.org/Howto:_Set_u ... yer_server
Normally, building and configuring fgms should take you about 5 minutes.
Let us know if you need any help though!
Also, it's a good idea to get in touch with the developers mailing list (actually, Curt), so that the mpserverXX.flightgear.org alias can be set up for your server.
Also, once your server is set up and running, you may want to add it to this list: http://wiki.flightgear.org/Howto:_Multiplayer