Pond + Stream Setup?

You could do a 2 pump set up, if you want. One pump (1000 gph min) for the full system, and perhaps another 500 gph to discharge right above the water fall to make it more impressive.
Use a hybrid pump. They are the most efficient for gallons moved per watt. That style of pump works better with somewhat larger pipe. For 1000 gph pump perhaps 1-1/2" PVC. 2000 gph, perhaps 2" pipe? When in doubt, over size it, anyway.
And if you need to make 90 degree turns get sweep 90s or use a couple of 45 degree fittings. The extra cost of the fittings is more than made up for with the reduced pressure loss of the gentler turn.

Rigid PVC or flex PVC are the most commonly used tubing/pipe in that size. These are completely fish safe when the PVC cement has cured.

Bio media can go wherever you want, but with plants, pots, soil and so on there are so many lodging sites that unless you are planning to way overstock the pond I would not go crazy about bio media. However, why not add perhaps about 50 gallons of volume at the very top? This would be a chamber for all the media you want, sponge, bio and anything else. Then the water falls into the stream and so on.

Hi Diana I think you helped me over on my post in APC. Thanks so much, I didn't even think about how I would do the turns. I'm going to Home Depot / Lowes this weekend to look at some supplies.

I will raise the waterfall chamber sufficiently to stack in a layer of sponge and bioballs!

I'm not sure what the difference of a hybrid pump is?

I was looking at this magnetic drive pump (mainly cause it was shiny)...
http://www.amazon.com/Danner-02650-...UTF8&qid=1345040203&sr=8-5&keywords=pond+pump

Here is a hybrid one for about the same price, more energy efficient?
http://www.amazon.com/Danner-20210-...F8&qid=1345040190&sr=8-2&keywords=hybrid+pump

Mag drive is one step better than the older pumps, Hybrid is even better.

Mag drives can usually pump the water to higher levels, so a chart showing head loss might look better on the mag drive, but you are not wanting to pump the water 10-20' up! A chart for a hybrid pump will not look so impressive after a fairly low cut off point. They are great at the lower head heights, though, which is exactly the height of most pond and stream set ups.
Look at the head loss at just a bit higher than your waterfall. Perhaps 50% higher, maybe not even that much. Pressure loss in the pipes can be minimized by going with larger diameter pipe, and Hybrid drive pumps benefit a lot from this.
When in doubt, a larger pump is better, because you can add a ball valve to reduce the flow, if you need to. In all the ponds I have built, pumps never seem to put out as many gph as they are rated for. If you wanted 2 pumps you might make them add up to about 2000 gph. This is a very good way to save electricity. 1000-1500 gph is very good circulation for fish and filter, but may not be quite as impressive a water fall. Adding a pump that discharges just above the water fall would make the water fall sound better.

Another filter option, look into a 55 gallon drum. This can be hidden somewhere near the pond, or even buried near the top of the water fall (perhaps in the hill you are building to make the water fall). Just make sure you can drain it through the bottom to flush it out once in a while.

Best waterfall:
Make the water shoot out into the air then fall into the pond. The hollow behind the falling water makes an echo chamber that intensifies the sound. Makes a much more impressive melody that just a rippling stream.

Had to run to work for a bit...
OK, in your drawing above you have a brown hatched area like a steep water-fall/white water stream.
That can work, but is very tricky for a first time pond builder to do it right.

Much easier:
Design a small pool at the top. Water from the pump enters through this. It can be a preformed filter/pool/overflow such as the box on the left in this link:
http://www.pondsupply.com/small_pond_kits.html
This spills into the top of the stream.

See the box (same link) on the right? That is a skimmer box, and acts like a swimming pool skimmer. Floating debris is picked up, and your pump can hide in there. You can build this into your lower pond.
I do not do it that way, I just have the pump in the pond itself.

And yes, I did a different sort of write up at APC. More details on how I made my pond and stream.

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.