I would plumb the skimmer so the discharge helps the stream look more impressive. Outlet at the top of the stream. You will need a baffle so the goldfish do not swim downstream. I could never keep Golds in my upper pond. Within a day or so they always found their way to the main pond.
The main filter and pump do not need to be located at the upper falls area. If you have another spot in the yard these can be remote, the same way swimming pool equipment is. Discharge would then be tucked into some sort of hill of rocks. Liner needs to go under this. The idea of remote equipment can offer several benefits:
No sound from the pump.
Access to electricity.
Easy to access the filter for cleaning. No need to camouflage it.
Easy access to the pump, it is not in a box.
Note that not all pumps are intended to be worked in such a way. You need one that will not burn out when it operates above the water line. If the remote location is roughly level with the pond that is best, if the location is slightly downhill then priming the pump is easy. If the location is too far downhill then you will lose too much pressure pumping the water back up hill.
Make sure to dig a big enough hole that when the power goes out the lower pond will hold all the water. A backflow device in the line may be needed to keep the water in the upper pond.
I would make a way to drain the upper pond separately, just in case you need to clean it without bothering the lower pond. I do not know if you want to plumb this in, or just plan on using a hose like a giant gravel vac.