Yeah, I've pierced aquifers from below a couple of times. It's actually easier than piercing an aquifer from above, because all the water falls out of your excavations instead of sitting there and blocking further progress.
Don't try a map edge fortification, it will be a water source on an ocean site.
What you need to do is dig down a level from where your dwarves will be coming in, and dig a tunnel into a 10x10 room with one more dug tile on the far corner from where water will come in. You put a 10x10 drawbridge into the room, flip it up with a lever, then put a pressure plate triggered by 0-6 water in that far tile and link it to the bridge. When the room fills up, the plate will untrigger and drop the drawbridge, crushing all water in the room; then the water on the plate will fall off, causing it to retrigger and reraise the bridge. It's a perpetual water smasher.
Then you just dig up a level, smooth all the walls, repeat. All the water falls into the smasher and gets out of your way.
It gets trickier if you're dealing with an aquifer in a soil level. Then you need to dig out the soil and replace it with walls, but if you do that, the dug out tiles end up having too much water to build in. You have to channel them, but if you haven't already dug out the walls below and smoothed everything that gets exposed, you end up with a bunch of extra water on the level below.
Basically, to dig a 1x1 stairwell in a soil aquifer level, you want to plan for a 3x3 stairwell on the level below; if that's soil too, then you want 5x5 on the level below that, and so on until you have a stairwell of constant dimensions throughout any stone aquifers and leading all the way into your water crusher. You'd be best advised to take it slowly and dig up one set of stairs at a time and smooth everything you see before digging another set of stairs.
Don't do Derakon's thing with the ramps and grates, you want to do up/down stairs leading directly into your drains or you'll end up with even more dangerous terrain cancellation spam than you're already going to have. You can grate over the stairwell at the dwarf-entry level if you're worried about dwarves falling in.