You don't. For one reason, it wouldn't be thread-safe. If you did somehow spec that a atom contained a map, it could change to an integer in the time it takes you to check the atom, and continue with your function.
One option, however, is to provide a validator to the atom. You could easily use partial to do this: (set-validator! my-atom (partial s/valid? :my-spec))
. Now the atom will fail to update unless the value conforms to :my-spec.
Another option is to add validation logic to all the functions that update the atom. Which of these two approaches works best depends on the application.