A metaroom is an area in a world, subdivided into rooms with doors between them. Often they have a music file associated with them; music tracks can be specified per-room, but the files themselves are usually per-metaroom.
Every metaroom in C3/DS has a position in the world (the Ark or the Capillata), and this position is not necessarily where they "should" go--the Creatures 3 environments are all arranged in a rough rectangle while the "main" part of the ship is just below them. A map of most of the metarooms can be found at the Norngarden website.
It seems that the "smaller" world is mostly full though there are a few gaps for small metarooms. However there is also a larger map with much more space, about 50 to 100 times as much. There must be some compatibility issues with this larger world but if there are, they are not known.