You would need to use drainage from below and it is fairly simple, that is, go under the aquifer using twinslit or whatever, then build a drainage shaft to the map edge (carved fortification), build an off valve (floodgate or hatch) and link it to a lever, and then punch an up/down stairwell into the bottom of tank. You will probably need a larger than 1x1 shaft, probably a 3x3 shaft at minimum - but it only needs to be that wide for 3 z-levels below the aquifer, just enough height to give dwarves access from below.
The tank will continually drain down the shaft allowing you to do some work. Then when work is done, shut of the valve so the tank refills.
Unfortunately, you will not be able to (easily) seal off the shaft at any point above the valve. You might succeed in building a retracting bridge across the shaft (or might not, falling water is tricky), but the moment it is completed it will be thoroughly flooded and you won't be able to link it to a lever or deconstruct it, so if you succeed, you won't have the ability to drain the tank anymore. So this might result in your tank having a deep shaft at the bottom. Might be a problem or might not be.
There is another way, and that is to dig a full size up from the drain (i.e. at least 3-z level below the aquifer, at that point it can narrow down to a 1 tile wide drainage shaft) say you want a 10x10 tank. Dig a 12x12 shaft of up/down stairs from 3z below the aquifer, through the aquifer, to the surface. Then wall off the aquifer on the top 2 z-levels (do this from the top down, to the bottommost level of the aquifer). Once the aquifer has been completely walled off you can floor/bridge off the appropriate level for the desired depth of your tank.
This method works great and I've used it to punch large sealed shafts through aquifers (i.e. for sunlit under aquifer gardens and stuff) and it'll work for a tank in the aquifer too.