After laying a first course of rocks in the front, cover them with a sheet of black plastic. Extend one end of the plastic up to the top of the plastic pot, while tucking the other over the lip of the preformed pond liner and down into the water. Then disguise the plastic with rocks, so that it wouldn't be visible in the pond. The plastic serves the purpose of catching more water than the rocks alone could and funnel it into the pond. Much of the water that would otherwise be lost to splashing strikes against this plastic and falls back into the pond, instead.
Also after laying the first course of rocks in front and just after laying the black plastic, lay one long, flat rock spanning them all and sitting right on top of that plastic. The long, flat rock juts out in the direction of the pond, forming an overhang. It will serve as a shelf for your first spillway rock, so it will be referred to as the "shelf rock."
Invert the flower pot and thread your tubing through the hole in its bottom. Place the pot on the ground (still inverted) at the center of what will be the rock waterfall structure. How far in back of the pond should this be? Well, that depends on the depth of your rocks. You'll want the rocks that face the pond to abut it; if possible, they should even overhang the pond slightly. So if the rocks you'll be using there are 8" in depth (i.e., front to back), the front side of the pot should be about 8" back from the edge of the pond.
How long should the tubing be? Leave yourself with a length that is longer than what you'll need, and trim later as necessary. This will make your job a lot easier! As to where to run it along the ground, choose either the left or the right side of the pond and rock waterfall. As a cosmetic touch at the end of the project, you can go back and hide it with stones and/or mulch.
Typically, when building rock walls, it's a good idea to stagger the seams. Of course, these will be very small rock walls, so it's not a structural concern here. Still, try to do some staggering, if only because it looks better.
As already mentioned in speaking of rock selection, after the first course of rocks in the front was down, you put one long flat rock spanning them all. Why? Because this rock's function is to form an overhang, it's a key piece in your cascade design. Using it as a shelf, you'll place your first spillway rock on it, in such a way that the spillway rock overhangs the pond even further.