Initial 2 paragraphs of ramble. Attempts of answers below that...
The main problem with power from the surface, in my view, is that the shaft needed for the axles also provide access to fliers and climbers. Water wheels are also vulnerable to building destroyers, and won't function while the stream is frozen in winter.
It is possible to (ab)use screw pumps to plug the shaft. Since screw pumps can be destroyed by building destroyers, the trick is to build the pump such that there is nowhere for a destroyer to stand (the instruction I received when I tried that with wind mills was 3 levels above ground), and obviously a housing to block access from all sides (only the pump output side is exposed, as well as that tile's top).
I've used water wheels a number of times, but I've then had them in the aquifer using a trick to induce flow in aquifers. I could have just channeled a flow from the aquifer to the edge and driven the wheels the normal way, but since flowing water has a negative FPS effect I use the trick, which probably is more work than the straightforward method anyway.
- You have to use a gear (or a machine) to change power transmission direction, so the same logic you used at the top is used at the bottom. So you build a horizontal train of axles from the water mill up to a gear and then build a vertical section (and a new gear everywhere you want to change direction).
When building the vertical section, you can only place axles either suspended from the top or supported from beneath, which means you can build at most two sections at a time (or use tricks with side supported gears midway). For the vertical section I build a staircase beside a shaft, to allow access to each tile for the building of the corresponding axle segment.
A gear at the top is supported if there is at least one horizontal axle (or machine/gear) beside it that's on solid ground/floor. If it's not supported, it will collapse immediately when the building finishes (such as building a floor from a bridge). Of course, the gear is also supported if hanging from something supported, but then it wouldn't be the top one...
- Note that a gear beside (horizontally or vertically) another gear can transfer power just fine if you need to bridge a single tile distance.
- Also note that magma pump stacks suffer the same support issues that axles do. It LOOKS like each pump is supported by a floor, but actually the whole pump is supported by the tile that has a hole under it for power distribution. So again, you can build from the top and bottom simultaneously if you've made sure the top is supported (typically a gear supported by a horizontal axle on ground/floor). The bottom is supported naturally, since you don't channel out the floor below the lowest pump (only the tile beside the pump where you get the magma) [which ought to be secured from access by magma sea creatures].