The proper positioning of the pump you choose to use will depend on whether or not you want to create a fountain or waterfall feature or want to just keep your pond well-circulated.
Submersible pumps are by far the most commonly used in most home-based pond keeping practices, and they are designed to be positioned underwater. They should be put at the bottom of the pond, but somewhere easy to access for maintenance purposes. Most come with an area at the top where a rope or a cord could be attached for easy removal from the pond, and you should be cautious to never lift a pump by its electrical cord, as this can be particularly dangerous.