xpCynic, The way Mondark did it involved pressure plates, which don't work. You're probably best off to have one lever for fill and one lever for empty and have it right next to the place the water comes from, so it's obvious what it does, and next to a spot where you can see how deep the water is.
By the way, you can use long series' of pumps to move water in faster. Also having a waterfall so the PC can get the hint would be a good idea.
If you do want to have it so you pull levers to specify how many level of water:
Build each layer so they have exactly the same number of tiles.
Build one cistern with that many tiles for each layer.
Make a series of pumps that allows each cistern to take water from the bottom layer and and water to the top layer.
Give each cistern a single lever. If it's pulled one way, the pumps leading to it are on and the ones leading away are off. If it's pulled the other way, it's switched.
By the way, you can turn pumps off by connecting a gear to something that uses too much power. See
Mechanical Logic for details. Also, rather than having two sets of pumps for each cistern, you can use one set of pumps and a hatch, so when the hatch is open the water drains one way, and when it's closed, but the pumps are on, it pumps the other way. Finally, if you want to make sure there's no evaporation, build all of the floors out of bars so the water's not just on the floor, and make each cistern two z-levels deep, but only use the top z-level. Since all of the bars have to be connected to walls, you'll have to make sections like this:
(= means bars, O means wall)
====O==
==O====
O====O=
===O===
=O====O
====O==
==O====
This is a cool thread, but I'm too much of a noob to join. I am allowed to give ideas though, right?
Have a lever that, when pulled, drops a donut shaped area around the PC to make them fall a z-level. Someone already suggested that part. Make it so this places them in a room with a floodgate and a lever, but no other way out. When they pull that lever it opens the floodgate, leading into a partially drained magma vent, with a bridge over it. It also opens a floodgate on the opposite side of the bridge, opens a cage on the other side of the door, and opens the retracting bridge that was keeping the magma vent from filling. This will leave the PC forced to fight a monster on a bridge over a slowly-filling magma vent.
As an added bonus, if the PC survives, try and distract them after they leave for long enough that the magma vent fills and the lava spills out of the opened floodgate.