For the 'sextant' measurement you need to press the 'z' button. Then you get the azimuth/altitude grid. Then you have to zoom in on the celestial object and 'shoot' against the nearest gridline.
I too had trouble getting Stellarium to accept a long/lat position through commandline parameters and config file. But the manual explains not everything works completely yet.
Maybe it's possible to add a 'city' location to the list with the sub's coordinates. And have Stellarium remember that as default location instead of Paris.
Unfortunately the older version (0.9 something) doesn't work with vista. Or my system anyway.
