First of all, pumps are effectively "firewalls" for water pressure. Whatever the pressure of the water is on their inward side, they reset to a fixed pressure on their output side. This is directional and allows you to control the flow of pressure. Water pressure should (and someone correct me if I am wrong here) only flow up to the level of the far side of the screw pump, after which point it equalizes out.
Secondly, one piece of advice I would have is to build a cistern somewhere higher than everything you want to provide with water, like a water tower. This will allow you a ready source of water you can unleash to flow down into all the places you need it. Make a pump stack from a primary water source (like a river) that will bring up enough water to fill it. Maybe have a raised aqueduct running from the pump stack to the cistern. Put another pump at the bottom edge of the cistern so you can draw water out when you need to.
Wind power is useful if you have it, if not then you will need to go with water power. The difficulty of using water power (unless you are abusing DF's lack of the conservation of energy) is that the source of power should not be too close to the place where water is being drawn, or the reduction in flowing water beneath the wheel will compromise the pump's ability to draw it as power cuts out. Either way, you will need some axles going about your plumbing levels. Try to keep the paths from your power sources to your pumps as straight and clear and with as few divergences as possible. The more corners and spots where you split power, the more you lose that power in the transmission.
You will need a drain for your sewers, somewhere for the wastewater to go. Either pump it back up and flow it down river from your input, or send it into a aquifer layer, or dig down and dump it into some out flowing pool or underground river in the caves. Otherwise you risk backfilling your fortress and the whole place is flooded.
Finally, pressure plates can be used to determine when "enough" water is in a particular spot. Tend on the side of caution by setting the water level over the pressure plate to trigger at a lower level than you think you might need. It will take a few ticks to send the shutoff signal, and in that time the water will keep pouring. Use a floodgate or door with a floor grate drain on the other side to flush the water to your outgoing plumbing when you are done. I might recommend you use baths that take a manual input the fill them, an automatic shut off that keeps them from getting too full, and another manual signal to empty them. No sense in trying to be too clever to make this fully automatic, or you could end up with unexpected results.