Both the place and the warren are pretty symbolic, so it's a good thing that the book is named after them. As a place, Watership Down is far from humanity, which is a good thing in this book. For instance, we hear all about how quiet the Down is:
Few places are far from human noise—cars, buses, motorcycles, tractors, lorries. […] During the last fifty years the silence of much of the country has been destroyed. But here, on Watership Down, there floated up only faint traces of the daylight noise below. (19.2)
Did you notice that all the noisy things that the narrator mentions are all big transportation machines? It's not just like "humans build noisy factories"—because if humans build a factory, the rabbits can move away from it. But a car or motorcycle can follow a rabbit.
That means that Watership Down is a great place for rabbits because it's far from humans (who aren't very good about taking care of nature). When Hazel's rabbits get to Watership Down, they no longer have to worry about humans, unless they decide to go raid a farm, but what stupid rabbit would do that?
And just as Hazel is almost an ideal Chief Rabbit, the Watership Down Warren is a pretty ideal warren. And we can learn a lot about the rabbits by looking at their warrens. The Efrafan rabbits, for example, aren't allowed to dig and expand their warren—so Efrafa is always the same warren, which makes it a nice symbol for how inflexible the politics of Efrafa are.
In comparison, Watership Down is very flexible, able to mix-and-match different styles together. So it seems pretty old-fashioned in most of its creation, like Sandleford Warren; but it's able to incorporate new designs, like the Great Burrow from Cowslip's warren. In fact, Watership Down Warren starts from some old warren that the rabbits find there, which is a nice symbol of how they use traditional techniques (or holes) in addition to digging new ones.
Even the discovery of Watership Down Warren is symbolic. Hazel notes that Fiver is responsible for them getting to this awesome place. Hazel even calls Fiver "Fiver-rah," meaning "Lord Fiver" (18.25). So the rabbits owe Watership Down to the special, psychic rabbit, right?
Ah, not so fast, because the narrator makes a big deal over the fact that the old holes that serve as the basis for Watership Down Warren were found by Hawkbit: "Thus it fell to one of the rank and file to make a lucky find that brought them at last to the downs" (18.42). So if you think about it (and we have, a lot), the Watership Down Warren seems like a joint effort of the unusual rabbits that get to be main characters (like Fiver and Hazel) and the regular characters that don't get a lot of attention (like Hawkbit, a regular "rank and file" rabbit). In that way, Watership Down Warren may be a symbol of cooperation and community.