In the movie
I am sure that it's intended to be all real; I don't remember anything that directly contradicts this interpretation.
While each main character reads or sees a story about the previous one (and is influenced by it, which is supposed to be the main point of it all), what we as audience see is what actually happened.
This distinction is pretty clear in the movie about Cavendish that Sonmi sees: the movie is cheesily dramatized, but different from what the audience is shown - there's even a direct cut between the two versions.
The only element that is a bit dubious is the birthmark shared by all the main characters, but I'd say that's too weak to conclude Zachary made it all up, especially since the other stories contain too many elements completely outside his sphere of experience.
In the book
It's a lot more complex here. There are at least two factors that contradict the straightforward interpretation:
- Vyvyan Ayrs mentions a dream he had, which is a pretty detailed description of Sonmi's working environment at Papa Song's. To accept that in-universe would require some sort of prescience.
- Unlike the movie, Luisa Rey's story ends with the conspiracy being exposed to the public and the president of the USA vowing to have it fully investigated. It's also a bigger scandal, with multiple murders and the involvement of a top-level politician. My point is that it's so big that Cavendish would have heard of it and couldn't accept the story as simple fiction (but that's what he does).
But I don't think the correct conclusion is that certain parts of the story are in-universe fiction and the others "real". There are too many cross-connections between the stories (Luisa Rey sees the actual ship Ewing travelled on, Meronym mentions Buenas Yerbas and even Swanneke, Cavendish mishears a taxi driver saying "exactly" as "Zachary", etc.). The biggest hint is Frobisher's description of the structure of his Cloud Atlas Sextet: it actually matches exactly the structure of the novel we're reading.
It's, of course, all fiction - one big story about people living at different times, but interconnected in various ways, not just through simple causality.