How DOES one pierce an aquifer?
How I did it, based off the "Double slit method" on the wiki
-Dig a 2x1 or 1x2 up/down stairway down into the first aquifer layer, so that the bottom stairway is flooded
-build two screw pumps, pulling from the wet stairway, and wall off and channel the output so it feeds directly into the aquifer layer elsewhere
-deconstruct/remove one of the stairways on the same z-level as one of the pumps, otherwise that pump won't work. But keep one so your dwarves have access
-Use a dwarf to power the now usable pump, one pump should be able to relatively drain the staircase.
-Send a dorf down to mine out a square adjacent to the wet staircase, and replace it with a contructed wall. Go one at a time, diagonal walls don't need to be touched. If the aquifer is a stone layer, you can smooth the existing walls rather than replace them.
-You will get suspensions on building the walls something fierce, but persevere and keep unsuspending it. As long as a dorf can touch the wall for a little while, some progress will be made on building that wall.
-Repeat until all non-diagonal walls are built/smoothed, rebuilding staircases if necessary to access the second pump. Once those walls are built, no new water will pour in.
-Proceed downward, leave a z-level between the aquifer and whatever you wish to build deeper.