I ran into a similar problem with my fortress involving flooding of unexpected portions. I dammed a river in the middle of winter, channeled it through a mostly unmined level into a room surrounding my central stairway, and then just let it pour down the shaft. At the bottom, there is a 3 tile wide channel leading to offscreen fortifications.
I noticed two things: regardless of how much water was falling down, and how full the channel was, as long as it was pressurized by the drop it would never overflow, BUT I had to make the drain TWO z levels below the normal shaft bottom to prevent the odd bit of water from escaping into the level above the drain channel. I am fairly certain that pressurized fluids can actively push fluid units rather than just "stacking". Second, I noticed that if I didn't depressurize the water by using diagonals, it would spray up and out of my well which fed off of the same system, albeit a different portion seperate from the waterfall/exit channel. I haven't seen a need to depressurize the exit channel, which should assuredly be a strait shot to the exit point. Pressure can't act on a diagonal, so putting a bend in the exit shaft may cause it to back up
so instead of
V
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use
V
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_________| |______________________|w|_________
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