In the case of the flatworld generator, you can specify addition world options to specify what type of layers to generate. These are the same options as can be seen in the 'Create new world - Customize' windows in the client. It is here that you can, for example, change the height of the flatworld, change block types or include populators such as ores, villages and trees. The format of the options is a bit vague, you can find more help on this subject on the Minecraft Wiki.