I think they are just there. Sometimes Atrus will write a world that has no-one in it at all, sometimes he writes a world where he finds a native population.
While it could be argued that people migrated to the older D'ni books, the ones that Atrus writes could not have this migration.
Also, the world where Atrus meets Catherine is written by Atrus' Father (if I remember correctly). There are no D'ni around at the time to populate it, so how did they get there?
I think each world is a unique and independent eco-system, meaning that life is bound to pop up on its own. The way the books are written it seems like they are simply linking in to an already existing world, so therefore life would already be evolving.
I dont remember there being a definitive answer to this, It's one of those things you are either supposed to figure out yourself, or there is no answer! Thats my opinion on it anyway.