I started working on a 3x3 site recently with an uncovered magma pipe in the middle and 5 tiles of underground river, coming south from the NW corner and hooking around the pipe to a chasm in the SE corner. I've already drained the pipe (though I had to un-drain it for a second to get a fire imp back in the magma without killing it) and it's staying steady at the bottom Z-level around 5/7. I set up a secondary pump and routed some water from the sealed-off UG river to make a small (though functional) obsidian factory around the chasm end of the river, which should double as a web-collection area when drained, though it could potentially grow tower caps as well when the obsidian is cleared out. I'm just starting to produce obsidian blocks to build everything with, and I'll move all my supplies down into the first levels of the chamber after they're properly constructed.
I'm building the fortress with a few rules in mind to force me to build things differently than I normally do. Firstly, I'm not building any hallways, just a 3x3 walkable balcony around the edge of the 19x19 central pit on each floor, all the way down to the magma vent itself. Secondly, I'm not building a vastly tall central staircase. Instead, I have a 9x9 spiral ramp structure three tiles wide going up the center of the entire structure connecting each floor. I can't think of any way to fit the tube's refilling into the design of the fortress as anything over than a doomsday flood, as it would render the central ramp unusable, stranding every dwarf on their individual level (or worse, individual rooms) unless I sealed it from the outside, which would ruin my security plan of shooting seigers on the spiral from the balcony.