I am writing a film report on Cloud Atlas (though the school system is different here, I would be in high school in the US, AFAIK) and I have to explain the title as part of this film report, but apart from the Cloud Atlas Sextet I can't remember any references to the title. The Atlas part I can interpret as a map of consequences of our actions, but I have no idea where the Clouds come from.
In an interview with Paris Review, Cloud Atlas author David Mitchell stated that the title was inspired by the piece of music of the same name by the Japanese composer Toshi Ichiyanagi, who was Yoko Ono’s first husband: "I bought the CD just because of that track's beautiful title."
Hugo Weaving, who plays the villain in all six parts of the film "Cloud Atlas" described the title thusly;
[When asked] "Why is it called 'Cloud Atlas?' " Weaving said. "The clouds being like souls and the breadth of humanity, all of the souls that are constantly shifting and changing through time," he explained. "Clouds shift their color and size and shape and come back."
"And the idea that our lives are not our own and every act out kindness out crime births your future," added Sarandon. "I think it's partially that because it's in the trailer," she said with a laugh.
Additionally, in the book (and film) one of the main characters, Frobisher develops a piece of music referred to as the "Cloud Atlas Sextet".
The author David Mitchell explains this in an interview with the BBC.
(copied from Wikipedia)
The title itself "Cloud Atlas," the cloud refers to the ever changing manifestations of the Atlas, which is the fixed human nature which is always thus and ever shall be. So the book's theme is predacity, the way individuals prey on individuals, groups on groups, nations on nations, tribes on tribes. So I just take this theme and in a sense reincarnate that theme in another context...
There is another mention of Cloud Atlas in the book. Perhaps somebody can help me with the exact quote, but in Sloosha's Crossin' an' Ev'rythin' After it is mentioned as being a literal atlas which the primitives use to navigate between the islands (as alluded to in real life for example by the Māori name for New Zealand: Aotearoa, "the land of the long white cloud").
I feel that the title Cloud Atlas refers to reincarnation of souls and how they navigate from where they are to where they are reincarnating. As an Atlas is a map and clouds are ever changing their shape and position I guess this I my simple explanation.