If you're doing it in an environment where water freezes, just dig out a pit 2 squares longer on each side than your intended passage through the aquifer. Do this by channeling one row at a time, from one direction to the other (i.e., left to right, top to bottom, etc) until you are one z-level above the water. Then, wait until the winter freeze before digging further. To avoid someone freezing themselves in the water as it freezes, channel out the floor one square at a time, that way the water can freeze before your dwarves step on it. As before, go one row at a time. If you have an open space instead of an ice floor, that's a glitch. Build a floor over the open space, then remove it, and the ice floor will be there like it's supposed to be.
To get through it, dig into your ice floor. Clear out everything except the outermost ring of ice (if you dig into it, water will flow into the square and refreeze; best case scenario you waste your time, worst case the poor miner is trapped in ice as he moves), then build walls adjacent to it (to prevent a thaw from melting this ice and the aquifer flooding your fort).
Diagram:
X is ice
= is the undug area around your passage
U is walls you built
- is the cleared passage for your staircase through the aquifer.
For example, a 5x5 pit would yield the following:
=======
=XXXXX=
=XUUUX=
=XU-UX=
=XUUUX=
=XXXXX=
=======
As you can see, to even get a 3x3 stairway, you'll have to START with a 7x7 pit.
If you're in an environment where it's too hot for water to ever freeze, good luck. You're going to have to either cheat/exploit, dig around the aquifer if you can where your multiple biomes cross, or (if that doesn't work/single biome embark/also not a cheater or exploiter) rig a pumping system to pump enough water out of the aquifer for your masons to VERY slowly smooth the walls or (in the frequent case of soil aquifers) build artificial walls, thus stopping the flow into the intended passage.
My first fort with an aquifer was, thankfully, one where the water only thaws 2 weeks in the summer in my northernmost biome. My southern two biomes were permafrost; I breached the aquifer there, and now it NEVER melts. I still built a wall, just in case. After all, water should never be trusted to behave itself when your fortress is involved.
EDIT: If all you want is ice, not a way through it, omit my earlier plans for building a stairway. Just dig down, channel away one square at a time, enjoy your new ice rink!