Is there an easy way to exclude the appendages like propeller shafts, rudders, stabilizers from the tanks and compartments? With the round shape of the hull in way of both it's difficult to define the extend of the tank to avoid intersection with the external (or internal in case of the shaft going through the tank) appendages.
The simplest way is to use fore/aft tapered takns (you can specify different values for top/bottom P/S for the fwd section of the tank and aft section)
If this is not sufficient, break you tank into several smaller linked tanks
Finally if none of the above work, use tank boundary surfaces (in Modeler type="Hull") to exclude the appendages, make the surface outside the main hull but not include the appendages. Make sure the surface forms a closed contour in Body Plan -- then use this as a boundary surface in the Stability tank definition