I don't know the -easiest- way, but here's how I did it:
I dug a small room off to the side of one of my major industrial centers (ok, major's probably pushing it... and I'm just starting out expanding past that "
Complete Newby Playalong" thread). The room was 3x3. I channeled (designate, channel) a 1x1 hole in the center. Unfortunately, this channeled straight down into mining tunnels I had built in the level below, and I didn't want those levels getting flooded (and I wanted the water to be lower than just one level, to slow down potential flooding, not that it actually worked), so I walled off this 'open space' I had just created and went a level lower (two from my well room) and dug a medium sized room directly beneath the well. Not centered, but I suppose it doesn't matter.
I then had two passageways, one north to a point ALMOST under the above-ground river, and one south to my stairs so that dwarves could get down into this future cistern easier. (This isn't actually the order I dug things in, but explaining it in this order will make it easier for you to understand.) I then put in three floodgates... one at the far far north end of the corridor, as a sort of master control for all water flow, so I can cut off all flow at any time I want to (as I'm planning on this one single northern corridor to be the primary artery for several water projects) and I link that floodgate to a lever two levels up in my extravagant dining/meeting room so it can be flipped at a moment's notice in case of emergencies. I put a second floodgate at the edge of the north part of the upcoming cistern, and a third floodgate at the south edge of the cistern. I plan on the southern most one (closest to my stairs) to be closed up permanently once I'm done constructing everything, and the one just north of that on the northern edge of the cistern to automatically close once the level of water in my cistern reaches a certain level, thereby POSSIBLY enabling a automated refilling system that doesn't require manual switch flipping. The automated northern floodgate will operate via a
pressure plate system you can read about.
On the western wall of my cistern, I now build a small tunnel and then a MUCH larger room. Larger than the cistern. My original plan for this room was for it to be an indoor fishing pond, if I could figure out some way of somehow populating the pond with fish, but as a result of something going horribly wrong with my automated pressure plate floodgate system, it's ended up being just a spilloff room. I suggest you have one too. Attach a floodgate to the tunnel connecting the cistern with the spilloff room, and attach a lever to it.
You're pretty much ready, assuming you've attached levers to everything, and that pressure plate to the cistern's northern floodgate. Open up the northern most floodgate (the master control one) and start creating/digging stairs up. Make sure you don't do what I did and dig straight up under what will eventually be wet dirt (I was still fine, somehow my dwarf got out from the water before it washed him back down the stairs into my cistern). Dig up a couple of squares just south of the river. (All directions in this guide assume your river is north of where you want your well. If it's not, you'll have to figure out how to flip the stuff around.) Once you've broken through the surface, CLOSE your master control switch, and then channel (designate, channel) to the river. Water should flow through your channel, to the stairs, down the stairs, all the way to your closed master control floodgate.
After that, you just have to get the water down to the cistern. I'm pretty sure you know how. I suggest having the spilloff room open and ready just in case the pressure plate fails like mine did. Observe the depth of the water with K (5/7 or 6/7 is enough in the cistern) and then shut off the spilloff rooms and the water flow once it's there. The well two levels above should no longer be labeled as 'dry' at that point.
If you did everything right, you should have an indoor well. If you did things wrong, water should be coming up through your well and into your fortress, flooding everything. Maybe you can make it to the master control switch in time!
