Great! It works! The first thing I noticed was that the tower I build, and which in my imagination was tall, was pretty stubby and short actually. It's because I imagined the distance between Z-levels to be about 1.5 times the size of the X,Y grid. It kinda puts things in perspective.
EDIT: Picture of my fortress.
You can see the river meandering through the zone, the brown depression in the right is an artificial lake, filled with water from the aquifer. Note that it has a built floor for the part that's over the river. In that part is a floor hatch, and to the left just below and behind the wall is a channel with a floodgate, this way I can empty the lake into the river whenever necessary. The tower will be home to the queen when she arrives, the top walls and ceiling are made of clear glass blocks. The holes in the walls of the top floor are clear glass windows. The opening at the foot of the tower is the only entrance to my fortress (waterways are sealed with fortifications). The ramp you see is a large paved road that crosses the river with a drawbridge, and heads into the hill, it comes out of the hill to the left, outside the picture, and to the rear. The road to the rear you can see as a large paved stone path crossing the river again and splitting off in two directions. One is the aqueduct, which is going to be build further out to the left as a bridge as well. The aqueduct is a pump-stack built into a tower on the river bank, with a subterranean connection to the river. It pumps through the duct into the hill, and becomes a waterfall through the dwarves' apartments' atrium. The waterfall drains into the aquifer. I considered drawing water from the aquifer for the waterfalls, for the sake of being independent of the outside world. I may implement that in the future. To the right of the queen's tower you can see a flat white area with a hole in it. It is the unfinished glass roof of my barracks, to prevent cave adaptation of my soldiers. The fact that it's unfinished is very clear on the inside, which is dripping in buzzard blood, spilled by soldiers pissed at being woken up on their break. The actual floor of the barracks is 4 Z-levels lower. The river has a dam made of floodgates under the bridge. Normally the river doesn't flow, but I'm considering mining out the downriver part of the zone (foreground of the picture) and submerging it.
EDIT: For those that want to get this to work on linux, I run three things:
First a script to allow programs to access each others memory.
sudo sysctl -w kernel.randomize_va_space=0
sudo sysctl -w kernel.yama.ptrace_scope=0
Then I run Dwarven Fortress by clicking the link in the application menu or in Nautilus. (running it from terminal gives memory access problems, see a few posts below.)
Then (after loading my game in DF) I run a script to start Overseer:
cd ~/Overseer
export LD_LIBRARY_PATH=`pwd`
./Overseer
sudo sysctl -w kernel.randomize_va_space=1
sudo sysctl -w kernel.yama.ptrace_scope=1
This script also disables the cross-process memory access after closing Overseer, since it's a pretty nasty security weakness.
Of course people who aren't particularly worried about security can simply allow the cross-process memory access once and not disable it after running overseer.
Those people who are worried about security can probably run the script to set the variables to 1 directly after starting DF.
NOTE: I run this in three scripts, since I tried to concatenate the first two, and noticed that Overseer couldn't access the memory of Dwarven Fortress.
My guess is:
Setting the variables only applies to processes started afterwards. As ./df is launched from the same script, it's running as a child process of the script (or somesuch) and thus isn't a process started after the variables have been altered.