I think I drowned a bit early on, but I've been pretty good about it since then. I've gotten pretty good at building underwater.
As for leaking.. yea, it can be a pain. It is all under city protection, so thankfully no one griefs it and leaves things all flooded, but except for the domes most of the city is underground (under the sea floor), so often I'll be working on something underground and discover that clearing space for a ceiling results in letting in water from outside. That can be a pain, but usually isn't hard to fix, just makes things take a bit longer.
That is one frustration about building this city, everything takes longer to do. I wish I had more done by now, but it is slow going, I don't have a whole lot of time, and I don't have as much help as I'd like.