Maybe I looked in the wrong places, but I couldn't find documentation for the multiworld feature.

Do I just put a copy of default.yml with just the RewardTable nodes I want to change in the worlds folder with the name of the world I want to affect the same as the name of the file?

Or do I have to create a new folder under worlds and then put another .yml file under that?

Definitely deficient on the multiworld documentation. Just copy default.yml to the worlds folder and rename it to the name of the world you want. For example, if my world is named "creature_world", then I would need the following:

plugins/ecoCreature/worlds/creature_world.yml

Added multiworld documentation to the dev bukkit homepage.

If I leave out nodes like System will they be inherited from the default.yml?

Unfortunately, not at the moment. The newer bukkit config allows for this type of functionality and I plan to take advantage of it when I revamp the config.