So, spring-data does some extra magic that helps with complex queries. It is strange at first and you totally skip it in the docs but it is really powerful and useful.
It involves creating a custom Repository and a custom `RepositoryImpl' and telling Spring where to find it. Here is an example:
Configuration class - point to your still-needed xml config with annotation pointing to your repositories package (it looks for *Impl classes automatically now):
@Configuration
@EnableJpaRepositories(basePackages = {"com.examples.repositories"})
@EnableTransactionManagement
public class MyConfiguration {
}
jpa-repositories.xml - tell Spring where to find your repositories. Also tell Spring to look for custom repositories with the CustomImpl file name:
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans" xmlns:jpa="http://www.springframework.org/schema/data/jpa"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:util="http://www.springframework.org/schema/util"
xsi:schemaLocation="http://www.springframework.org/schema/data/mongo http://www.springframework.org/schema/data/jpa/spring-jpa.xsd
    http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
    http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd">
<jpa:repositories base-package="com.example.repositories" repository-impl-postfix="CustomImpl" />
</beans>
MyObjectRepository - this is where you can put annotated and unannotated query methods. Note how this repository interface extends the Custom one:
@Transactional
public interface MyObjectRepository extends JpaRepository<MyObject, Integer>, MyObjectRepositoryCustom {
    List<MyObject> findByName(String name);
    @Query("select * from my_object where name = ?0 or middle_name = ?0")
    List<MyObject> findByFirstNameOrMiddleName(String name);
}
MyObjectRepositoryCustom - repository methods that are more complex and cannot be handled with a simple query or an annotation:
public interface MyObjectRepositoryCustom {
    List<MyObject> findByNameWithWeirdOrdering(String name);
}
MyObjectRepositoryCustomImpl - where you actually implement those methods with an autowired EntityManager:
public class MyObjectRepositoryCustomImpl implements MyObjectRepositoryCustom {
    @Autowired
    private EntityManager entityManager;
    public final List<MyObject> findByNameWithWeirdOrdering(String name) {
        Query query = query(where("name").is(name));
        query.sort().on("whatever", Order.ASC);
        return entityManager.find(query, MyObject.class);
    }
}
Amazingly, this all comes together and methods from both interfaces (and the CRUD interface, you implement) all show up when you do:
myObjectRepository.
You will see:
myObjectRepository.save()
myObjectRepository.findAll()
myObjectRepository.findByName()
myObjectRepository.findByFirstNameOrMiddleName()
myObjectRepository.findByNameWithWeirdOrdering()
It really does work. And you get one interface for querying. spring-data really is ready for a large application. And the more queries you can push into simple or annotation only the better off you are.
All of this is documented at the Spring Data Jpa site.