Sorry for any confusion. My pond and stream has 2 waterfalls, and I may not have been clear about the plumbing details. The upper waterfall would be in the box shown in that link. Then the stream. The stream ends above the pond, and there is another drop into the pond.
1) Both pumps can be in the skimmer, or just the main pump. The secondary pump can be in the pond near the base of the lower water fall, or in some other part of the pond that has less than ideal water movement. If you have a pond with curving edges or a dense area with lots of plants perhaps in pots, hide the smaller pump in this area. It could be placed in a planting basket with just a little bit of thin sponge.
2) A vinyl tube carries the water from the smaller pump to a spot near the top of the lower waterfall so it looks more impressive. Hide the tubing in the rocks if it is anywhere near the water fall. Take it outside the pond only if necessary. Plants and rocks are good at hiding some tubing.
3) Often the skimmer would be on the opposite side of the pond from the lower waterfall. The pipe will exit the skimmer from the main pump, go outside the pond and feed the waterfall up at the top of the stream. Almost all the pipe is buried, just enough is exposed to include a ball valve and union, and these might fit in the sump with the pump. If you also place the smaller pump in here it also could go in the same trench until it gets slightly above the lower falls, then it has to go into the stream to add to that lower falls.
4) The smaller pump does not need to run all the time. It is more for show. It will have just enough sponge around it to keep the pump free of debris, but is not the main filtration.