In the server.properties file, there should be a line that says "level type" like so:
#Minecraft server properties
#Thu Mar 22 16:21:37 PDT 2012
server-port=25565 level-type=DEFAULT-------------If you want flat, set to FLAT.
motd=A Minecraft Server
Then, if you have already generated a regular world, delete the "world" folder. When the server restarts it will generate a new, flat world.
Hope this helps!
What I do is. Go to Single Player create a new world name it "world" and set the settings to SUPERFLAT and let it generate and when it's done go to your .minecraft folder (Hoping that you know where that is.) Go to saves. Copy the "world" folder and import it to the server.