What is the problem here?
It's not so far, you have already dug a channel.
Maybe dig a sewer reservoir/system a level (or more) below the one of the river level as that is the same as your main settlement.
channel a shaft directly down through all Z-layers from your well-head.
You don't need water before constructing the well...for a waterwheel I think you do need running water.
Make sure you wall off / forbidden-door any maintenance connections to your fortress on the flooded sewer levels.
Also installing a floodgate at a bottleneck before flooding the system is highly advised to prevent the entire fort from flooding in case of a construction error or simmilar.
Also a wall-grate in the inlet channel prevents dangerous guppies etal from getting in via that route. probably a fortification would do the trick as well, although there are rumours of water creatures bypassing these.
--
I'm just finishing the final touches to my deep well, it goes down almost to the bottom-level and has a staircase running around the central shaft, fed from a stream on the wrong side of a volcano on a 7or 8wide map.
(Unfortunately I misused ramps to 'connect' the several layers before channelling out the UP/DOWN staircase running along the well axis.
code:
XXXXX
X...X
X.x.X
Xr_rX
XXXXX
r=ramp up or down, _ floor, .=openspace, x =stairs.
and round at 90deg rotation per Z-level. Obviously, in hindsight, when you remove the stairs, the ramps dunt work as they are constructed against the outside wall. Now replacing the ramps with stairs, but slow progress without the stairs for access.have fun.
Losing a fort to drowning is a learning experience, don't get too attached to your first dorfs, you can always restart or reclaim with a fresh batch.
(taking a highly skilled mechanic to start drainage efforts right away. )
ps when working on a cliffy map with thirsty dwarfs and a river on the wrong side of the map, DONT dig from two sides at once when creating your mains. Your thirsty dorfs will use the access ladders to the waterside digs for fieldtrips. This takes up alot of dwarftime. And they naturally confound the matter by following the streambed from the bottom to the most northers upstream spot to drink. tripling their traveltime. >sigh<
Good brewers prevented my for from death by hikers.