External pond pumps are ideal for large ponds with a bottom drain. In Koi ponds because of the large volume of waste it is a great idea to go for a gravity fed bottom drain which means all the debris that accumulates on the bottom of the pond is sucked into the refuge pipe. You need to ensure that your filter chamber is kept at the same water level as your pond water, that way the water is continually moved from the filter to the pond and from the pond to the filter.
For an external pump your pond water level and your filter water level are kept balanced rather like a bathroom u-bend, ensuring that the water levels go from the pond to the filter and vice versa.
Having an external pump is a cleaner way of pumping water out of your pond as it means all of the sludge at the bottom of your pond is naturally managed.