In Watership Down, are the epigraphs before each chapter related more to the story or to larger literary themes?
Each epigraph (short quote before a chapter) in the novel is related in some way to the themes of the story in that chapter; they shed light on the ideas which will be presented and add depth to both character and plot. For example, in Chapter 13, the epigraph comes from Alfred, Lord Tennyson's poem "The Lotos-Eaters."
In the afternoon they came unto a land
In which it seemed always afternoon.
All round the coast the languid air did swoon,
Breathing like one that hath a weary dream.
Tennyson, "The Lotus-Eaters"
The poem describes travelers who become addicted to the opiate flower of the lotus, which causes them to fall into a trance and despite danger, believe their lives to be better off. Similarly, in that chapter, the traveling rabbits have discovered what seems to be an ideal warren, full of fat rabbits with plenty of food and a human who shoots all the predators who come near.
"He kills owls too. We never need to dig. No one's dug in my lifetime. A lot of the burrows are lying empty, you know: rats, live in one part, but the man kills them as well, when he can. We don't need expeditions. There's better food here than anywhere else. Your friends will be happy living here."
(Adams, Watership Down, Google Books)
However, it comes out that the human is actually farming the wild rabbits; he sets out snares among the food to harvest rabbits when they come to feed. The poem alludes to the fact that this seemingly-safe place is actually a place of great and accepted danger; the rabbits are content to live in relative safety, and consider the occasional sacrifice of one of their own to be acceptable, if it means that they don't have to live in fear of wild animals. Like these rabbits, the men in Tennyson's poem decide that living without their loved ones or former lives, and with nobody knowing their fate, is acceptable as long as they can continue consuming the lotos flowers. Neither will ever be truly safe, but their illusion is enough for their superficial contentment.
Therefore, the epigraph allows those versed in poetry to gain a deeper layer of understanding when the secret of the "safe" warren is revealed. By connecting the two literary works, it also allows the reader to further recognize these themes and tropes when reading other works.